Citrus Sinensis ID: 023463

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Local Sequence Feature Prediction

Residue Number Marker
--------10--------20--------30--------40--------50--------60--------70--------80--------90-------100-------110-------120-------130-------140-------150-------160-------170-------180-------190-------200-------210-------220-------230-------240-------250-------260-------270-------280--
Protein Sequence
MTHDPEILTPEEHFYFLKMGRKCKNYVPVGRRGIYQGVILNMHLHWKKHQTLKVIVKTFSAEEVKEIAAELARLTGGIVLEIHEENTIIMYRGKNYAQPPTEIMSPRITLSRKKALDKSKYRDGLRAVKKYIPKLEQELELLRAQAETRSENRSDAAEDVQNTELDKPDFGSIPSMMECSENDPTTESLMASDSEDLSDIFETDSETETEEKAELRPLYLDQFDKFPVQNDEEHEDFEEHLRQISIDSRNAKSLGKDEDSSHFDEVDKMFLRAASLLKKQKR
Secondary Structure (PSIPRED)
cccccccccHHHHHHHHHHHHcccccccccccccHHHHHHHHHHHHHHcccEEEEEccccHHHHHHHHHHHHHHHccEEEEEEEccEEEEEEcccccccccccccccccccHHHHHHHHHHHHHHHHHHHcHHHHHHHHHHHHHHHHHHHHHcccHHHHHccccccccccccccccccccccccccccccccccccccccccccccHHHHHHHHccccccccccccccccccccccHHHHHHHHHHcccccccccccccccccccHHHHHHcHHHHHHHHcc
Secondary Structure Prediction (SSPRO)
cccccccccHHHHHHHHHHcHccccccccccccccHHHHHHHHHHHHcccEEEEEEccccHHHHHHHHHHHHHHcccEEEEEEcccEEEEEEcccccccccccccccccccHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHcHHHHHHccccccccccHcccccHcHcccccccccccccccccccccccccccccccccccccccccHHHHccccccccccHcHHHHHHHHHHHccccccccccccccccHHHHHHHHHHHHHHHHHHcc
Coil and Loop (DISEMBL)
mthdpeiltpeeHFYFLKMGrkcknyvpvgrrgiYQGVILNMHLHWKKHQTLKVIVKTFSAEEVKEIAAELARLTGGIVLEIHEENTIImyrgknyaqppteimspritlsrkkaldkskyrDGLRAVKKYIPKLEQELELLRAQAETrsenrsdaaedvqnteldkpdfgsipsmmecsendptteslmasdsedlsdifetdseteteekaelrplyldqfdkfpvqndeehEDFEEHLRQISIDsrnakslgkdedsshfdEVDKMFLRAASLLKKQKR
Flexible Loop (DISEMBL)
mthdpeiltpeEHFYFLKMGRKCKNYVPVGRRGIYQGVILNMHLHWKKHQTLKVIVKTFSAEEVKEIAAELARLTGGIVLEIHEENTIImyrgknyaqppteimspritlsrkkaldkskyrdglravKKYIPKLEQELELLRAQAetrsenrsdaaedvqnteldkpdfgsipSMMECSENDPTTESLMASDSEDLSDIFETDseteteekaelrplyldQFDKFPVQNDEEHEDFEEHLRQisidsrnakslgkdedsshfdevDKMFLRAASLLKKQKR
Low Complexity Region (SEG)
MTHDPEILTPEEHFYFLKMGRKCKNYVPVGRRGIYQGVILNMHLHWKKHQTLKVIVKTFSAEEVKEIAAELARLTGGIVLEIHEENTIIMYRGKNYAQPPTEIMSPRITLSRKKALDKSKYRDGLRAVKKYIPKleqelellraqaeTRSENRSDAAEDVQNTELDKPDFGSIPSMMECSENDPTTESLMASDSEDLSDIFETDSETETEEKAELRPLYLDQFDKFPVQNDEEHEDFEEHLRQISIDSRNAKSLGKDEDSSHFDEVDKMFLRAASLLKKQKR
Disordered region (IsUnstruct)
**********EEHFYFLKMGRKCKNYVPVGRRGIYQGVILNMHLHWKKHQTLKVIVKTFSAEEVKEIAAELARLTGGIVLEIHEENTIIMYRGKNYA***************************LRAVKKYIP*****************************************************************************************************************************************************
Disordered Region (DISOPRED)
**HDPEILTPEEHFYFLKMGRKCKNYVPVGRRGIYQGVILNMHLHWKKHQTLKVIVKTFSAEEVKEIAAELARLTGGIVLEIHEENTIIMYRGKNYAQPPTEIMSPRITLSRKKA*******************LE*ELEL****************************************************************************LYL******************************************FDEVDKMFLRAASLL*****
Disordered Region (DISEMBL)
MTHDPEILTPEEHFYFLKMGRKCKNYVPVGRRGIYQGVILNMHLHWKKHQTLKVIVKTFSAEEVKEIAAELARLTGGIVLEIHEENTIIMYRGKNYAQPPTEIMSPRITLSRKKALDKSKYRDGLRAVKKYIPKLEQELELLRAQ***************QNTELDKPDFGSIPSMMECSENDPTTESLMASDSEDLSDI************AELRPLYLDQFDKFPVQNDEEHEDFEEHLRQISIDSRN************FDEVDKMFLRAASLLKKQKR
Disordered Region (DISPRO)
*****EILTPEEHFYFLKMGRKCKNYVPVGRRGIYQGVILNMHLHWKKHQTLKVIVKTFSAEEVKEIAAELARLTGGIVLEIHEENTIIMYRGKNYAQPPTEIMSPRITLSRKKALDKSKYRDGLRAVKKYIPKLEQELELLRAQAETRSE*R************************************************************ELRPLYLDQFDKFPV****EHEDFEEHLRQISID************SSHFDEVDKMFLRAASLLKK***
Transmembrane Helix (TMHMM)
oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Transmembrane Helix (HMMTOP)
ooooooooooooooooooooooooooHHHHHHHHHHHHHHHHHHiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiii
Transmembrane Helix (MEMSAT)
iiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiihhhhhhhhhhhhhhhhhhhhhhoooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
TM Helix, Signal Peptide (MEMSAT_SVM)
iiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiihhhhhhhhhhhhhhhhooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
TM Helix, Signal Peptide (Phobius)
oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Signal Peptide (SignalP HMM Mode)
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Signal Peptide (SignalP NN Mode)
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Coiled Coils (COILS)
MTHDPEILTPEEHFYFLKMGRKCKNYVPVGRRGIYQGVILNMHLHWKKHQTLKVIVKTFSAEEVKEIAAELARLTGGIVLEIHEENTIIMYRGKNYAQPPTEIMSPRITLSRKKALDKSKYRDGxxxxxxxxxxxxxxxxxxxxxxxxxxxxRSDAAEDVQNTELDKPDFGSIPSMMECSENDPTTESLMASDSEDLSDIFETDSETETEEKAELRPLYLDQFDKFPVQNDEEHEDFEEHLRQISIDSRNAKSLGKDEDSSHFDEVDKMFLRAASLLKKQKR
Positional Conservation
no confident homologs detected

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Close Homologs for Annotation Transfer

Close Homologs in SWISS-PROT Database Detected by BLAST

Original result of BLAST against SWISS-PROT Database

ID	Length	Definition	RBH(Q2H)	RBH(H2Q)	Q cover	H cover	Identity	E-value
Query	282	2.2.26 [Sep-21-2011]
Q67XL4	444	Uncharacterized CRM domai	yes	no	0.953	0.605	0.664	1e-94
Q9FYT6	715	Chloroplastic group IIA i	N/A	no	0.404	0.159	0.403	3e-15
Q6YYA3	725	Chloroplastic group IIA i	no	no	0.404	0.157	0.394	4e-15
Q9LF10	720	Chloroplastic group IIA i	no	no	0.496	0.194	0.326	7e-14
Q5VMQ5	701	CRS2-associated factor 1,	no	no	0.319	0.128	0.307	5e-07
Q84N49	674	CRS2-associated factor 1,	N/A	no	0.315	0.132	0.326	3e-06
Q6Z4U2	428	CRS2-associated factor 1,	no	no	0.319	0.210	0.268	2e-05
Q0J7J7	366	CRS2-associated factor 2,	no	no	0.258	0.199	0.283	0.0003
Q84N48	611	CRS2-associated factor 2,	N/A	no	0.315	0.145	0.271	0.0004
Q657G7	607	CRS2-associated factor 2,	no	no	0.234	0.108	0.289	0.0004

>sp|Q67XL4|Y3544_ARATH Uncharacterized CRM domain-containing protein At3g25440, chloroplastic OS=Arabidopsis thaliana GN=At3g25440 PE=2 SV=1

 Score =  346 bits (888), Expect = 1e-94,   Method: Compositional matrix adjust.
 Identities = 190/286 (66%), Positives = 221/286 (77%), Gaps = 17/286 (5%)

Query: 2   THDPEILTPEEHFYFLKMGRKCKNYVPVGRRGIYQGVILNMHLHWKKHQTLKVIVKTFSA 61
           THDPEILTPEEHFY+LKMG KCKNYVPVGRRGIYQGVILNMHLHWKKHQTL+V++KTF+ 
Sbjct: 171 THDPEILTPEEHFYYLKMGLKCKNYVPVGRRGIYQGVILNMHLHWKKHQTLQVVIKTFTP 230

Query: 62  EEVKEIAAELARLTGGIVLEIHEENTIIMYRGKNYAQPPTEIMSPRITLSRKKALDKSKY 121
           +EVKEIA ELARLTGGIVL++HE NTIIMYRGKNY QPPTEIMSPRITL RKKALDKSK 
Sbjct: 231 DEVKEIAVELARLTGGIVLDVHEGNTIIMYRGKNYVQPPTEIMSPRITLPRKKALDKSKC 290

Query: 122 RDGLRAVKKYIPKLEQELELLRAQAETRSENRSDAAEDVQ--NTELDKPDFGSIPSMMEC 179
           RD LRAV+KYIP+LEQEL+LL+AQAET+ +  +   +D Q  + EL K    S   + + 
Sbjct: 291 RDALRAVRKYIPRLEQELQLLQAQAETKRDYTNVKVDDNQERSEELKKIIERSEECLEDE 350

Query: 180 SENDPTTESLMASDSEDLSDIFETDSETETEEKAELRPLYLDQFDKFPVQNDEEHEDFEE 239
            E D     L A+DS DLSDIFETDSE E + K E RPL+L++F+KFP  N+ E EDF  
Sbjct: 351 QEEDEAGLEL-ATDS-DLSDIFETDSELE-DAKTE-RPLFLEEFEKFPAINNREDEDFG- 405

Query: 240 HLRQISIDSRNAKSLGKDED---SSHFDEVDKMFLRAASLLKKQKR 282
                  D   AKS G++ D   S +FDEVDKMFLRAA LLKK++R
Sbjct: 406 -------DLGKAKSEGEENDDDKSPNFDEVDKMFLRAAFLLKKKRR 444

Arabidopsis thaliana (taxid: 3702)

>sp|Q9FYT6|CRS1_MAIZE Chloroplastic group IIA intron splicing facilitator CRS1, chloroplastic OS=Zea mays GN=CRS1 PE=1 SV=1

 Score = 82.8 bits (203), Expect = 3e-15,   Method: Compositional matrix adjust.
 Identities = 48/119 (40%), Positives = 69/119 (57%), Gaps = 5/119 (4%)

Query: 4   DPEILTPEEHFYFLKMGRKCKNYVPVGRRGIYQGVILNMHLHWKKHQTLKVIVKTFSAEE 63
           D E LT EE   F ++GRK    V +GRRGI+ GVI  +H HWK  + +KVI K     +
Sbjct: 560 DREHLTEEEKIMFRRIGRKMDGLVLLGRRGIFDGVIEEIHQHWKHKEVVKVITKQNQTRQ 619

Query: 64  VKEIAAELARLTGGIVLEIHEENT---IIMYRGKNYAQPPTEIMSPRITLSRKKALDKS 119
           +   A+ L   TGGI++ + +  T   II+YRGKNY +P     S    L++++AL +S
Sbjct: 620 IMYAASLLEVETGGILIAVEKLTTSHAIILYRGKNYRRPAKSSFSN--LLTKREALRRS 676

Required for the splicing of group IIA introns in chloroplasts, and especially for atpF, by regulating the intron folding. Forms splicing particles with RNA. Also involved in chloroplast protein translation.

Zea mays (taxid: 4577)

>sp|Q6YYA3|CRS1_ORYSJ Chloroplastic group IIA intron splicing facilitator CRS1, chloroplastic OS=Oryza sativa subsp. japonica GN=Os08g0360100 PE=2 SV=1

 Score = 82.0 bits (201), Expect = 4e-15,   Method: Compositional matrix adjust.
 Identities = 47/119 (39%), Positives = 70/119 (58%), Gaps = 5/119 (4%)

Query: 4   DPEILTPEEHFYFLKMGRKCKNYVPVGRRGIYQGVILNMHLHWKKHQTLKVIVKTFSAEE 63
           D E+LT EE   F K+G K   +V +GRRG+++GVI  +H HWK  + +KVI K   A +
Sbjct: 562 DRELLTEEERRIFRKIGLKMDEHVLLGRRGVFEGVIEEIHQHWKHKEVVKVITKQNQASQ 621

Query: 64  VKEIAAELARLTGGIVLEIHEENT---IIMYRGKNYAQPPTEIMSPRITLSRKKALDKS 119
           +   +  L   TGG ++ I    T   II+YRGKNY +P     +P   L++++AL +S
Sbjct: 622 ITYTSMMLEVETGGTLIAIERFTTSHAIILYRGKNYRRPTKS--APSNLLTKREALQRS 678

Required for the splicing of group IIA introns in chloroplasts, by regulating the intron folding. Forms splicing particles with RNA. Also involved in chloroplast protein translation.

Oryza sativa subsp. japonica (taxid: 39947)

>sp|Q9LF10|CRS1_ARATH Chloroplastic group IIA intron splicing facilitator CRS1, chloroplastic OS=Arabidopsis thaliana GN=At5g16180 PE=2 SV=2

 Score = 78.2 bits (191), Expect = 7e-14,   Method: Compositional matrix adjust.
 Identities = 47/144 (32%), Positives = 81/144 (56%), Gaps = 4/144 (2%)

Query: 4   DPEILTPEEHFYFLKMGRKCKNYVPVGRRGIYQGVILNMHLHWKKHQTLKVIVKTFSAEE 63
           D EILT EE     ++G K  + + +GRRG++ GV+  +H HWK  +  KVI        
Sbjct: 568 DIEILTNEERECLRRIGLKMNSSLVLGRRGVFFGVMEGLHQHWKHREVAKVITMQKLFSR 627

Query: 64  VKEIAAELARLTGGIVLEIH---EENTIIMYRGKNYAQPPTEIMSPRITLSRKKALDKSK 120
           V   A  L   + G+++ I    E + I++YRGKNY +P +++M+  + L+++KAL +S 
Sbjct: 628 VVYTAKALETESNGVLISIEKLKEGHAILIYRGKNYKRPSSKLMAQNL-LTKRKALQRSV 686

Query: 121 YRDGLRAVKKYIPKLEQELELLRA 144
               L ++K +  + E+ +E L+ 
Sbjct: 687 VMQRLGSLKFFAYQRERAIEDLKV 710

Required for the splicing of group IIA introns in chloroplasts, by regulating the intron folding. Forms splicing particles with RNA. May also be involved in chloroplast protein translation.

Arabidopsis thaliana (taxid: 3702)

>sp|Q5VMQ5|CAF1P_ORYSJ CRS2-associated factor 1, chloroplastic OS=Oryza sativa subsp. japonica GN=Os01g0495900 PE=2 SV=1

 Score = 55.1 bits (131), Expect = 5e-07,   Method: Compositional matrix adjust.
 Identities = 28/91 (30%), Positives = 47/91 (51%), Gaps = 1/91 (1%)

Query: 6   EILTPEEHFYFLKMGRKCKNYVPVGRRGIYQGVILNMHLHWKKHQTLKVIVKTFSAEEVK 65
           E LT EE    +K   K K  + +GR G+   ++ N+H HWK+ +  K+  K     ++ 
Sbjct: 183 EPLTKEEVDELVKATLKTKRQLNIGRDGLTHNMLENIHSHWKRKRVCKIKCKGVCTVDMD 242

Query: 66  EIAAELARLTGGIVLEIHEENTIIMYRGKNY 96
            +  +L    GG V+  H+   I ++RG+NY
Sbjct: 243 NVCQQLEEKVGGKVIH-HQGGVIFLFRGRNY 272

Required for the splicing of group IIB introns in chloroplasts. Forms splicing particles with CRS2. Interacts with RNA and confers intron specificity of the splicing particles.

Oryza sativa subsp. japonica (taxid: 39947)

>sp|Q84N49|CAF1P_MAIZE CRS2-associated factor 1, chloroplastic OS=Zea mays GN=CAF1 PE=1 SV=1

 Score = 52.8 bits (125), Expect = 3e-06,   Method: Compositional matrix adjust.
 Identities = 30/92 (32%), Positives = 48/92 (52%), Gaps = 3/92 (3%)

Query: 6   EILTPEEHFYFLKMGRKCKNYVPVGRRGIYQGVILNMHLHWKKHQTLKVIVKTFSAEEVK 65
           E LT EE    +K   K K  + +GR G+   ++ N+H HWK+ +  K+  K     ++ 
Sbjct: 183 EPLTKEEVSELVKGSLKSKRQLNMGRDGLTHNMLENIHSHWKRKRVCKIKCKGVCTIDMD 242

Query: 66  EIAAELARLTGGIVLEIHEENTII-MYRGKNY 96
            I  +L    GG V  IH +  +I ++RG+NY
Sbjct: 243 NICHQLEEKVGGKV--IHRQGGVIFLFRGRNY 272

Required for the splicing of group IIB introns in chloroplasts. Forms splicing particles with CRS2. Interacts with RNA and confers intron specificity of the splicing particles.

Zea mays (taxid: 4577)

>sp|Q6Z4U2|CAF1M_ORYSJ CRS2-associated factor 1, mitochondrial OS=Oryza sativa subsp. japonica GN=Os08g0174900 PE=2 SV=1

 Score = 50.1 bits (118), Expect = 2e-05,   Method: Compositional matrix adjust.
 Identities = 25/93 (26%), Positives = 50/93 (53%), Gaps = 3/93 (3%)

Query: 6   EILTPEEHFYFLKMGRK--CKNYVPVGRRGIYQGVILNMHLHWKKHQTLKVIVKTFSAEE 63
           E LTP E  + +   +K   K  + +GR G+   ++ ++H HWK  + ++V        +
Sbjct: 155 EPLTPAERAFLVSKCQKSRTKKQINLGRDGLTHNMLNDIHNHWKNDEAVRVKCLGVPTVD 214

Query: 64  VKEIAAELARLTGGIVLEIHEENTIIMYRGKNY 96
           ++ +  +L   TGG+++  H    +I+YRG++Y
Sbjct: 215 MQNVCHQLEDKTGGLIIHRH-GGQLILYRGRHY 246

May be involved for the splicing of group IIB introns in mitochondrions.

Oryza sativa subsp. japonica (taxid: 39947)

>sp|Q0J7J7|CAF2M_ORYSJ CRS2-associated factor 2, mitochondrial OS=Oryza sativa subsp. japonica GN=Os08g0188000 PE=2 SV=2

 Score = 45.8 bits (107), Expect = 3e-04,   Method: Compositional matrix adjust.
 Identities = 21/74 (28%), Positives = 39/74 (52%), Gaps = 1/74 (1%)

Query: 23  CKNYVPVGRRGIYQGVILNMHLHWKKHQTLKVIVKTFSAEEVKEIAAELARLTGGIVLEI 82
           C   + +G+ G+   +I ++H HWK+ + +++        ++  I   L   TGG V+  
Sbjct: 162 CSRQINLGKGGVTHNMIDDIHNHWKRAEAVRIKCLGVPTLDMDNICFHLEDKTGGKVI-Y 220

Query: 83  HEENTIIMYRGKNY 96
              N +I+YRG+NY
Sbjct: 221 RNINILILYRGRNY 234

May be involved for the splicing of group IIB introns in mitochondrions.

Oryza sativa subsp. japonica (taxid: 39947)

>sp|Q84N48|CAF2P_MAIZE CRS2-associated factor 2, chloroplastic OS=Zea mays GN=CAF2 PE=1 SV=1

 Score = 45.8 bits (107), Expect = 4e-04,   Method: Compositional matrix adjust.
 Identities = 25/92 (27%), Positives = 45/92 (48%), Gaps = 3/92 (3%)

Query: 6   EILTPEEHFYFLKMGRKCKNYVPVGRRGIYQGVILNMHLHWKKHQTLKVIVKTFSAEEVK 65
           E LTP E    +K        + +GR G+   ++  +H HW++ +  KV  +     ++K
Sbjct: 232 EPLTPSEVRALVKPHISHNRQLNIGRDGLTHNMLEMIHCHWRRQEICKVRCRGVPTVDMK 291

Query: 66  EIAAELARLTGGIVLEIHEENTII-MYRGKNY 96
            +   L   +GG V  IH    ++ +YRG++Y
Sbjct: 292 NLCYHLEEKSGGKV--IHRVGGVVFLYRGRHY 321

Required for the splicing of group IIB introns in chloroplasts. Forms splicing particles with CRS2. Interacts with RNA and confers intron specificity of the splicing particles.

Zea mays (taxid: 4577)

>sp|Q657G7|CAF2P_ORYSJ CRS2-associated factor 2, chloroplastic OS=Oryza sativa subsp. japonica GN=Os01g0323300 PE=2 SV=1

 Score = 45.4 bits (106), Expect = 4e-04,   Method: Compositional matrix adjust.
 Identities = 20/69 (28%), Positives = 37/69 (53%), Gaps = 3/69 (4%)

Query: 29  VGRRGIYQGVILNMHLHWKKHQTLKVIVKTFSAEEVKEIAAELARLTGGIVLEIHEENTI 88
           +GR G+   ++  +H HW++ +  KV  +     ++K +   L   +GG V  IH    +
Sbjct: 251 IGRDGLTHNMLEMIHCHWRRQEICKVRCRGVPTVDMKNLCYHLEEKSGGKV--IHRVGGV 308

Query: 89  I-MYRGKNY 96
           + +YRG+NY
Sbjct: 309 VFLYRGRNY 317

Required for the splicing of group IIB introns in chloroplasts. Forms splicing particles with CRS2. Interacts with RNA and confers intron specificity of the splicing particles.

Oryza sativa subsp. japonica (taxid: 39947)

Close Homologs in the Non-Redundant Database Detected by BLAST

Original result of BLAST against Nonredundant Database

GI	Length	Definition	Q cover	H cover	Identity	E-value
Query	282
297739537	331	unnamed protein product [Vitis vinifera]	0.992	0.845	0.706	1e-115
225448146	401	PREDICTED: uncharacterized CRM domain-co	0.992	0.698	0.706	1e-115
255572670	458	conserved hypothetical protein [Ricinus	0.989	0.609	0.706	1e-114
224132018	413	predicted protein [Populus trichocarpa]	0.964	0.658	0.675	1e-108
356498434	383	PREDICTED: uncharacterized CRM domain-co	0.975	0.718	0.663	1e-106
357439975	443	CRM domain-containing protein, putative	0.971	0.618	0.659	1e-104
356501797	382	PREDICTED: uncharacterized CRM domain-co	0.953	0.704	0.681	1e-104
449458069	500	PREDICTED: uncharacterized CRM domain-co	0.992	0.56	0.629	1e-101
357439925	472	CRM domain-containing protein, putative	0.971	0.580	0.601	7e-99
297831446	1055	predicted protein [Arabidopsis lyrata su	0.943	0.252	0.657	1e-94

>gi|297739537|emb|CBI29719.3| unnamed protein product [Vitis vinifera]

 Score =  419 bits (1077), Expect = e-115,   Method: Compositional matrix adjust.
 Identities = 209/296 (70%), Positives = 244/296 (82%), Gaps = 16/296 (5%)

Query: 2   THDPEILTPEEHFYFLKMGRKCKNYVPVGRRGIYQGVILNMHLHWKKHQTLKVIVKTFSA 61
           THDPEILTPEEHF+FLKMG KCKNYVP+GRRGIYQGVILNMHLHWKKHQTL+V+VKTFS 
Sbjct: 37  THDPEILTPEEHFFFLKMGLKCKNYVPIGRRGIYQGVILNMHLHWKKHQTLQVVVKTFSP 96

Query: 62  EEVKEIAAELARLTGGIVLEIHEENTIIMYRGKNYAQPPTEIMSPRITLSRKKALDKSKY 121
           EEVKEIA ELARLTGGIVL+IHEENTIIMYRGKNY+QPPTEIMSPRITLSRKKALDKSKY
Sbjct: 97  EEVKEIAVELARLTGGIVLDIHEENTIIMYRGKNYSQPPTEIMSPRITLSRKKALDKSKY 156

Query: 122 RDGLRAVKKYIPKLEQELELLRAQAETRSENRSDAAEDVQNTELDKPDFGSIPSMM---- 177
           RDGLRAV+KYIP+LE +LELL+AQA+ ++EN+++A ED QN  +D  +   I ++     
Sbjct: 157 RDGLRAVRKYIPRLEGDLELLQAQAKMQAENKTEAVEDFQNANIDSINSQGISNLQPENS 216

Query: 178 -----------ECSENDPTTESLMASDSEDLSDIFETDSETETEEKAELRPLYLDQFDKF 226
                      E SE +  T+S   S SE LSDIFE+DS+T+T+EKAE + LYL++F+KF
Sbjct: 217 DKLRELLAGNNESSEEESLTDSGTESCSEALSDIFESDSDTDTKEKAE-QLLYLNEFEKF 275

Query: 227 PVQNDEEHEDFEEHLRQISIDSRNAKSLGKDEDSSHFDEVDKMFLRAASLLKKQKR 282
           PV++D E EDFEEHLRQIS DSR AKSL KD D    DEVD+MFLRAASLLKK++R
Sbjct: 276 PVESDGEPEDFEEHLRQISADSRKAKSLEKDADLPQLDEVDQMFLRAASLLKKKRR 331

Source: Vitis vinifera

Species: Vitis vinifera

Genus: Vitis

Family: Vitaceae

Order: Vitales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|225448146|ref|XP_002263852.1| PREDICTED: uncharacterized CRM domain-containing protein At3g25440, chloroplastic-like [Vitis vinifera]

 Score =  419 bits (1077), Expect = e-115,   Method: Compositional matrix adjust.
 Identities = 209/296 (70%), Positives = 244/296 (82%), Gaps = 16/296 (5%)

Query: 2   THDPEILTPEEHFYFLKMGRKCKNYVPVGRRGIYQGVILNMHLHWKKHQTLKVIVKTFSA 61
           THDPEILTPEEHF+FLKMG KCKNYVP+GRRGIYQGVILNMHLHWKKHQTL+V+VKTFS 
Sbjct: 107 THDPEILTPEEHFFFLKMGLKCKNYVPIGRRGIYQGVILNMHLHWKKHQTLQVVVKTFSP 166

Query: 62  EEVKEIAAELARLTGGIVLEIHEENTIIMYRGKNYAQPPTEIMSPRITLSRKKALDKSKY 121
           EEVKEIA ELARLTGGIVL+IHEENTIIMYRGKNY+QPPTEIMSPRITLSRKKALDKSKY
Sbjct: 167 EEVKEIAVELARLTGGIVLDIHEENTIIMYRGKNYSQPPTEIMSPRITLSRKKALDKSKY 226

Query: 122 RDGLRAVKKYIPKLEQELELLRAQAETRSENRSDAAEDVQNTELDKPDFGSIPSMM---- 177
           RDGLRAV+KYIP+LE +LELL+AQA+ ++EN+++A ED QN  +D  +   I ++     
Sbjct: 227 RDGLRAVRKYIPRLEGDLELLQAQAKMQAENKTEAVEDFQNANIDSINSQGISNLQPENS 286

Query: 178 -----------ECSENDPTTESLMASDSEDLSDIFETDSETETEEKAELRPLYLDQFDKF 226
                      E SE +  T+S   S SE LSDIFE+DS+T+T+EKAE + LYL++F+KF
Sbjct: 287 DKLRELLAGNNESSEEESLTDSGTESCSEALSDIFESDSDTDTKEKAE-QLLYLNEFEKF 345

Query: 227 PVQNDEEHEDFEEHLRQISIDSRNAKSLGKDEDSSHFDEVDKMFLRAASLLKKQKR 282
           PV++D E EDFEEHLRQIS DSR AKSL KD D    DEVD+MFLRAASLLKK++R
Sbjct: 346 PVESDGEPEDFEEHLRQISADSRKAKSLEKDADLPQLDEVDQMFLRAASLLKKKRR 401

Source: Vitis vinifera

Species: Vitis vinifera

Genus: Vitis

Family: Vitaceae

Order: Vitales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|255572670|ref|XP_002527268.1| conserved hypothetical protein [Ricinus communis] gi|223533361|gb|EEF35112.1| conserved hypothetical protein [Ricinus communis]

 Score =  417 bits (1073), Expect = e-114,   Method: Compositional matrix adjust.
 Identities = 209/296 (70%), Positives = 242/296 (81%), Gaps = 17/296 (5%)

Query: 2   THDPEILTPEEHFYFLKMGRKCKNYVPVGRRGIYQGVILNMHLHWKKHQTLKVIVKTFSA 61
           THDPEILTPEEHF+FLKMG KCKNYVPVGRRGIYQGVILNMHLHWKKHQT++V+VKTFS 
Sbjct: 165 THDPEILTPEEHFFFLKMGLKCKNYVPVGRRGIYQGVILNMHLHWKKHQTVQVVVKTFSP 224

Query: 62  EEVKEIAAELARLTGGIVLEIHEENTIIMYRGKNYAQPPTEIMSPRITLSRKKALDKSKY 121
           EEVKEIAAELARLTGGIVL+IHEENTIIMYRGKNY+QPPTEIMSPRITLSRKKALDKSKY
Sbjct: 225 EEVKEIAAELARLTGGIVLDIHEENTIIMYRGKNYSQPPTEIMSPRITLSRKKALDKSKY 284

Query: 122 RDGLRAVKKYIPKLEQELELLRAQAETRSENRSDAAEDVQNTELDKPDFGSIPSMM---- 177
           RDGLRAV+ YIP+LEQ+LELL+ Q+  ++E  S +AE+   T+ D  + G +PS      
Sbjct: 285 RDGLRAVRNYIPRLEQDLELLKVQSMGKAECGSASAEETLYTD-DGAESGGVPSTPLENS 343

Query: 178 -----------ECSENDPTTESLMASDSEDLSDIFETDSETETEEKAELRPLYLDQFDKF 226
                      ECSE +   +  M SDSEDLSDIFETDS+TETE+K + RPLYL++F KF
Sbjct: 344 EKLKKITDGQEECSEEESPMDLGMLSDSEDLSDIFETDSDTETEDKVK-RPLYLEEFKKF 402

Query: 227 PVQNDEEHEDFEEHLRQISIDSRNAKSLGKDEDSSHFDEVDKMFLRAASLLKKQKR 282
           P+Q +EE EDFEEHLRQ+S+DSR  +S  KD D   FDEVD++FLRAASLLKK+KR
Sbjct: 403 PIQGNEEPEDFEEHLRQLSVDSRKVESSEKDSDIPSFDEVDRLFLRAASLLKKKKR 458

Source: Ricinus communis

Species: Ricinus communis

Genus: Ricinus

Family: Euphorbiaceae

Order: Malpighiales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|224132018|ref|XP_002321235.1| predicted protein [Populus trichocarpa] gi|222862008|gb|EEE99550.1| predicted protein [Populus trichocarpa]

 Score =  395 bits (1016), Expect = e-108,   Method: Compositional matrix adjust.
 Identities = 202/299 (67%), Positives = 243/299 (81%), Gaps = 27/299 (9%)

Query: 2   THDPEILTPEEHFYFLKMGRKCKNYVPVGRRGIYQGVILNMHLHWKKHQTLKVIVKTFSA 61
           THDPEILTPEEHF+FLKMG KCKNYVPVGRRGIYQGVILNMHLHWKKHQTLKV+VKTF+ 
Sbjct: 124 THDPEILTPEEHFFFLKMGLKCKNYVPVGRRGIYQGVILNMHLHWKKHQTLKVVVKTFTP 183

Query: 62  EEVKEIAAELARLTGGIVLEIHEENTIIMYRGKNYAQPPTEIMSPRITLSRKKALDKSKY 121
           EEVKEIAAELAR TGGIVL+IHEENTIIMYRGKNY+QPPTEIMSPR+TLSRKKALDKSK 
Sbjct: 184 EEVKEIAAELARFTGGIVLDIHEENTIIMYRGKNYSQPPTEIMSPRVTLSRKKALDKSKC 243

Query: 122 RDGLRAVKKYIPKLEQELELLRAQAETRS-----ENRSDAAEDVQNTE-----LDKPDFG 171
           RDGLRA+++YIP+L+Q+LELL A+A  ++     E+RS +++ ++N+E     +D+ D  
Sbjct: 244 RDGLRALRRYIPRLQQDLELLHARAGGKTDIDGAESRSISSKQLENSEKLKEIIDRQD-- 301

Query: 172 SIPSMMECSENDPTTESLMASDSEDLSDIFETDSETETEEKAELRPLYLDQFDKFPVQND 231
                 E SE+ P T+  +ASDSEDLSDIFETDS+ +TEE ++ RPLYL++F+KF V+ D
Sbjct: 302 ------EGSEDGPDTDLGIASDSEDLSDIFETDSDADTEETSK-RPLYLEEFEKFSVEAD 354

Query: 232 EEHEDFEEHLRQISIDSRNAKSLGK--------DEDSSHFDEVDKMFLRAASLLKKQKR 282
            E EDFEEHLRQIS+ S+   + GK        D DS  FDEVD+MFLRAASLLK++KR
Sbjct: 355 GEPEDFEEHLRQISLGSKKGVTSGKDVDIPTGVDVDSPSFDEVDRMFLRAASLLKRKKR 413

Source: Populus trichocarpa

Species: Populus trichocarpa

Genus: Populus

Family: Salicaceae

Order: Malpighiales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|356498434|ref|XP_003518057.1| PREDICTED: uncharacterized CRM domain-containing protein At3g25440, chloroplastic-like, partial [Glycine max]

 Score =  389 bits (999), Expect = e-106,   Method: Compositional matrix adjust.
 Identities = 195/294 (66%), Positives = 236/294 (80%), Gaps = 19/294 (6%)

Query: 2   THDPEILTPEEHFYFLKMGRKCKNYVPVGRRGIYQGVILNMHLHWKKHQTLKVIVKTFSA 61
           THDPEILTPEEHF+FLKMG K KNYVPVGRRGIYQGVILNMHLHWKKHQTLKV+VKTFSA
Sbjct: 92  THDPEILTPEEHFFFLKMGLKSKNYVPVGRRGIYQGVILNMHLHWKKHQTLKVVVKTFSA 151

Query: 62  EEVKEIAAELARLTGGIVLEIHEENTIIMYRGKNYAQPPTEIMSPRITLSRKKALDKSKY 121
           EEVKEIAAELARL+GGIVL+IHE+NTIIMYRGKNY+QPPTEIMSPR++LSRKKALDKSKY
Sbjct: 152 EEVKEIAAELARLSGGIVLDIHEDNTIIMYRGKNYSQPPTEIMSPRVSLSRKKALDKSKY 211

Query: 122 RDGLRAVKKYIPKLEQELELLRAQAETRSENRSDAAEDVQNTELDKPDFGSIPS------ 175
           RD LRAV++YIP+LEQELE+LRAQ ++ +E+ +DAAE +QN+  +  + GSI +      
Sbjct: 212 RDALRAVRRYIPRLEQELEILRAQFKSSAESNTDAAEAIQNSGRESIESGSISNFQLQNS 271

Query: 176 -----MMEC----SENDPTTESLMASDSEDLSDIFETDSETETEEKAELRPLYLDQFDKF 226
                MM      +E++    S + SDS+ LSDIFETDS+TE   K E +PLYLD+FD F
Sbjct: 272 YKDREMMNVNIGSTEDETDMNSELDSDSDKLSDIFETDSDTENFVKEE-KPLYLDEFDNF 330

Query: 227 PVQNDEEHEDFEEHLRQISIDSRNAKSLGKDEDSSHFDEVDKMFLRAASLLKKQ 280
           P Q+D E  DFEEH+RQ+S+ S+N   + KD++    DEVDK+FL+A S LKK+
Sbjct: 331 PEQSDGEMNDFEEHMRQMSLKSKN---MEKDDNLPKLDEVDKIFLQATSFLKKK 381

Source: Glycine max

Species: Glycine max

Genus: Glycine

Family: Fabaceae

Order: Fabales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|357439975|ref|XP_003590265.1| CRM domain-containing protein, putative [Medicago truncatula] gi|355479313|gb|AES60516.1| CRM domain-containing protein, putative [Medicago truncatula]

 Score =  383 bits (983), Expect = e-104,   Method: Compositional matrix adjust.
 Identities = 196/297 (65%), Positives = 237/297 (79%), Gaps = 23/297 (7%)

Query: 3   HDPEILTPEEHFYFLKMGRKCKNYVPVGRRGIYQGVILNMHLHWKKHQTLKVIVKTFSAE 62
           HDPEILTPEEHF+FLKMG K KNYVPVGRRGIYQGVILNMHLHWKKHQTL+V+VKTFSAE
Sbjct: 153 HDPEILTPEEHFFFLKMGLKSKNYVPVGRRGIYQGVILNMHLHWKKHQTLQVVVKTFSAE 212

Query: 63  EVKEIAAELARLTGGIVLEIHEENTIIMYRGKNYAQPPTEIMSPRITLSRKKALDKSKYR 122
           EVKEIA ELARLTGGIVL IHEE+TIIMYRGKNY+QPPTEIMSPR+TL RKKALDKSKYR
Sbjct: 213 EVKEIATELARLTGGIVLGIHEEDTIIMYRGKNYSQPPTEIMSPRVTLPRKKALDKSKYR 272

Query: 123 DGLRAVKKYIPKLEQELELLRAQAETRSENRSDAAEDVQ-------------NTELDKPD 169
           DGLRAV++YIPKLEQELE+LRAQ ++ +E+ ++AAE +Q             N +L+K D
Sbjct: 273 DGLRAVRRYIPKLEQELEILRAQFQSTAESNTEAAEGIQISDKVSVEPSSVSNLQLEKLD 332

Query: 170 FGSIPSMME----CSENDPTTESLMASDSEDLSDIFETDSETETEEKAELRPLYLDQFDK 225
              + +M      CSE++   +S + S S+ LSDIFETDS+TE   K E +PLYLD+F+ 
Sbjct: 333 --KVGAMFNDNNSCSEDEAHMDSDLDSYSDKLSDIFETDSDTEDLVKEE-KPLYLDEFNN 389

Query: 226 FPVQNDEEHEDFEEHLRQISIDSRNAKSLGKDEDSSHFDEVDKMFLRAASLLKKQKR 282
           FP Q+D + +DFEEHL+QIS +S+N   + KD D   FDEVD++FLRAAS LKK+++
Sbjct: 390 FPEQSDGDTDDFEEHLQQISYNSKN---MEKDADLPKFDEVDQIFLRAASFLKKKRK 443

Source: Medicago truncatula

Species: Medicago truncatula

Genus: Medicago

Family: Fabaceae

Order: Fabales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|356501797|ref|XP_003519710.1| PREDICTED: uncharacterized CRM domain-containing protein At3g25440, chloroplastic-like [Glycine max]

 Score =  382 bits (982), Expect = e-104,   Method: Compositional matrix adjust.
 Identities = 190/279 (68%), Positives = 229/279 (82%), Gaps = 10/279 (3%)

Query: 2   THDPEILTPEEHFYFLKMGRKCKNYVPVGRRGIYQGVILNMHLHWKKHQTLKVIVKTFSA 61
           THDPEILTPEEHF+FLKMG K KNYVPVGRRGIYQGVILNMHLHWKKHQTLKV+VKTFSA
Sbjct: 112 THDPEILTPEEHFFFLKMGLKSKNYVPVGRRGIYQGVILNMHLHWKKHQTLKVVVKTFSA 171

Query: 62  EEVKEIAAELARLTGGIVLEIHEENTIIMYRGKNYAQPPTEIMSPRITLSRKKALDKSKY 121
           EEVKEIA ELARL+GGIVL+IHE+NTIIMYRGKNY+QPPTEIMSPR++LSRKKALDKSKY
Sbjct: 172 EEVKEIATELARLSGGIVLDIHEDNTIIMYRGKNYSQPPTEIMSPRVSLSRKKALDKSKY 231

Query: 122 RDGLRAVKKYIPKLEQELELLRAQAETRSENRSDAAEDVQNTELDKPDFGSIPSMMECSE 181
           RD LRAV+++IP+LEQELE+LRAQ ++ +E+ +DAAE +QN      D       + C+E
Sbjct: 232 RDALRAVRRHIPRLEQELEILRAQFKSSAESNTDAAEAIQNNRERMND------NIGCTE 285

Query: 182 NDPTTESLMASDSEDLSDIFETDSETETEEKAELRPLYLDQFDKFPVQNDEEHEDFEEHL 241
           ++    S + SDS+ LSDIFETDS+TE   K E +PLYLD+FD FP Q+D E  DFEEHL
Sbjct: 286 DETDMNSELDSDSDKLSDIFETDSDTENFIKEE-KPLYLDEFDNFPEQSDGEMNDFEEHL 344

Query: 242 RQISIDSRNAKSLGKDEDSSHFDEVDKMFLRAASLLKKQ 280
           RQ+S+ S+N   + K+++    DEVDK+FL+A S LKK+
Sbjct: 345 RQMSLKSKN---MEKEDNLPKLDEVDKIFLQATSFLKKK 380

Source: Glycine max

Species: Glycine max

Genus: Glycine

Family: Fabaceae

Order: Fabales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|449458069|ref|XP_004146770.1| PREDICTED: uncharacterized CRM domain-containing protein At3g25440, chloroplastic-like [Cucumis sativus] gi|449516505|ref|XP_004165287.1| PREDICTED: uncharacterized CRM domain-containing protein At3g25440, chloroplastic-like [Cucumis sativus]

 Score =  374 bits (960), Expect = e-101,   Method: Compositional matrix adjust.
 Identities = 187/297 (62%), Positives = 233/297 (78%), Gaps = 17/297 (5%)

Query: 2   THDPEILTPEEHFYFLKMGRKCKNYVPVGRRGIYQGVILNMHLHWKKHQTLKVIVKTFSA 61
           THDPEILTPEEHFYFLKMG K KNYVPVGRRGIYQGVILNMHLHWKKHQT+KV+VKTFS 
Sbjct: 205 THDPEILTPEEHFYFLKMGIKGKNYVPVGRRGIYQGVILNMHLHWKKHQTVKVVVKTFSP 264

Query: 62  EEVKEIAAELARLTGGIVLEIHEENTIIMYRGKNYAQPPTEIMSPRITLSRKKALDKSKY 121
           EEVKEIAAELARLTGG+VL+IHEE+TIIMYRGKNY+QPPTEIMSPR++LSRKKALDKSKY
Sbjct: 265 EEVKEIAAELARLTGGLVLDIHEEDTIIMYRGKNYSQPPTEIMSPRVSLSRKKALDKSKY 324

Query: 122 RDGLRAVKKYIPKLEQELELLRAQAETRSENRSDAAEDVQNTELDKPDFGSIPSM----- 176
           RDGLRAV+K+IPKLEQEL  L++QA+   ++  ++ E +Q T  D     +I S+     
Sbjct: 325 RDGLRAVRKHIPKLEQELRFLQSQAKLNCKSNGESVEHMQETVDDTNKSKAISSLNLENL 384

Query: 177 -----------MECSENDPTTESLMASDSEDLSDIFETDSETETEEKAELRPLYLDQFDK 225
                       + S++    ++ M+SDSEDLSD+FETD ++E +EK E +PL+L +F+ 
Sbjct: 385 DDSSNAMRSVSKDWSDDSSPIDTGMSSDSEDLSDMFETDIDSEADEKME-KPLFLKEFEN 443

Query: 226 FPVQNDEEHEDFEEHLRQISIDSRNAKSLGKDEDSSHFDEVDKMFLRAASLLKKQKR 282
           F  + ++E ED  + LRQIS+DS+ AK L  D +S  FDEVD++FLR+ASLLKK++R
Sbjct: 444 FAAETEDEIEDLSDQLRQISMDSKQAKILENDVNSPEFDEVDRLFLRSASLLKKKRR 500

Source: Cucumis sativus

Species: Cucumis sativus

Genus: Cucumis

Family: Cucurbitaceae

Order: Cucurbitales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|357439925|ref|XP_003590240.1| CRM domain-containing protein, putative [Medicago truncatula] gi|355479288|gb|AES60491.1| CRM domain-containing protein, putative [Medicago truncatula]

 Score =  366 bits (939), Expect = 7e-99,   Method: Compositional matrix adjust.
 Identities = 196/326 (60%), Positives = 237/326 (72%), Gaps = 52/326 (15%)

Query: 3   HDPEILTPEEHFYFLKMGRKCKNYVPVGRRGIYQGVILNMHLHWKKHQTLKVIVKTFSAE 62
           HDPEILTPEEHF+FLKMG K KNYVPVGRRGIYQGVILNMHLHWKKHQTL+V+VKTFSAE
Sbjct: 153 HDPEILTPEEHFFFLKMGLKSKNYVPVGRRGIYQGVILNMHLHWKKHQTLQVVVKTFSAE 212

Query: 63  EVKEIAAELARLTGGIVLEIHEENTIIMYRGKNYAQPPTEIMSPRITLSRKK-------- 114
           EVKEIA ELARLTGGIVL IHEE+TIIMYRGKNY+QPPTEIMSPR+TL RKK        
Sbjct: 213 EVKEIATELARLTGGIVLGIHEEDTIIMYRGKNYSQPPTEIMSPRVTLPRKKVLHVPKDC 272

Query: 115 ---------------------ALDKSKYRDGLRAVKKYIPKLEQELELLRAQAETRSENR 153
                                ALDKSKYRDGLRAV++YIPKLEQELE+LRAQ ++ +E+ 
Sbjct: 273 LHHTIKDCFTFLFAYFPSLISALDKSKYRDGLRAVRRYIPKLEQELEILRAQFQSTAESN 332

Query: 154 SDAAEDVQ-------------NTELDKPDFGSIPSMME----CSENDPTTESLMASDSED 196
           ++AAE +Q             N +L+K D   + +M      CSE++   +S + S S+ 
Sbjct: 333 TEAAEGIQISDKVSVEPSSVSNLQLEKLD--KVGAMFNDNNSCSEDEAHMDSDLDSYSDK 390

Query: 197 LSDIFETDSETETEEKAELRPLYLDQFDKFPVQNDEEHEDFEEHLRQISIDSRNAKSLGK 256
           LSDIFETDS+TE   K E +PLYLD+F+ FP Q+D + +DFEEHL+QIS +S+N   + K
Sbjct: 391 LSDIFETDSDTEDLVKEE-KPLYLDEFNNFPEQSDGDTDDFEEHLQQISYNSKN---MEK 446

Query: 257 DEDSSHFDEVDKMFLRAASLLKKQKR 282
           D D   FDEVD++FLRAAS LKK+++
Sbjct: 447 DADLPKFDEVDQIFLRAASFLKKKRK 472

Source: Medicago truncatula

Species: Medicago truncatula

Genus: Medicago

Family: Fabaceae

Order: Fabales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|297831446|ref|XP_002883605.1| predicted protein [Arabidopsis lyrata subsp. lyrata] gi|297329445|gb|EFH59864.1| predicted protein [Arabidopsis lyrata subsp. lyrata]

 Score =  352 bits (902), Expect = 1e-94,   Method: Compositional matrix adjust.
 Identities = 188/286 (65%), Positives = 224/286 (78%), Gaps = 20/286 (6%)

Query: 2    THDPEILTPEEHFYFLKMGRKCKNYVPVGRRGIYQGVILNMHLHWKKHQTLKVIVKTFSA 61
            THDPEILTPEEHFY+LKMG KCKNYVPVGRRGIYQGVILNMHLHWKKHQTL+V++KTF+ 
Sbjct: 785  THDPEILTPEEHFYYLKMGLKCKNYVPVGRRGIYQGVILNMHLHWKKHQTLQVVIKTFTP 844

Query: 62   EEVKEIAAELARLTGGIVLEIHEENTIIMYRGKNYAQPPTEIMSPRITLSRKKALDKSKY 121
            +EV EIA ELARLTGGIVL++HE NTIIMYRGKNY QPPTEIMSPRITL RKKALDKSK 
Sbjct: 845  DEVNEIAVELARLTGGIVLDVHEGNTIIMYRGKNYVQPPTEIMSPRITLPRKKALDKSKC 904

Query: 122  RDGLRAVKKYIPKLEQELELLRAQAETRSENRSDAAEDVQ--NTELDKPDFGSIPSMMEC 179
            RD LRAV+KYIP+LEQEL+LL+AQAET+ E  +   +D+Q  + EL K    S   + + 
Sbjct: 905  RDALRAVRKYIPRLEQELQLLQAQAETKREYLNVKVDDIQERSDELKKIIERSEECLED- 963

Query: 180  SENDPTTESLMASDSEDLSDIFETDSETETEEKAELRPLYLDQFDKFP-VQNDEEHEDFE 238
             E +    S +A+DS DLSDIFETDSE E E+   +RPL+L++F+KFP + N+ E EDF 
Sbjct: 964  EEEEEDAGSELATDS-DLSDIFETDSELEDEKT--VRPLFLEEFEKFPAINNNREDEDFG 1020

Query: 239  EHLRQISIDSRNAKSLGKDED--SSHFDEVDKMFLRAASLLKKQKR 282
            +           AKS G++ D  S +FDEVDKMFLRAASLLKK++R
Sbjct: 1021 K-----------AKSEGEENDDKSPNFDEVDKMFLRAASLLKKKRR 1055

Source: Arabidopsis lyrata subsp. lyrata

Species: Arabidopsis lyrata

Genus: Arabidopsis

Family: Brassicaceae

Order: Brassicales

Phylum: Streptophyta

Superkingdom: Eukaryota

---

Prediction of Gene Ontology (GO) Terms

Close Homologs with Gene Ontology terms Detected by BLAST

Original result of BLAST against Gene Ontology (AMIGO)

ID	Length	Definition	Q cover	H cover	Identity	E-value
Query	282
TAIR|locus:2094438	444	LOH1 "LAG One Homologue 1" [Ar	0.943	0.599	0.619	8.2e-83
TAIR|locus:2056558	372	AT2G28480 [Arabidopsis thalian	0.730	0.553	0.377	1.1e-34
TAIR|locus:2091458	491	AT3G27550 [Arabidopsis thalian	0.460	0.264	0.492	4.5e-34
TAIR|locus:2123276	343	AT4G13070 [Arabidopsis thalian	0.460	0.379	0.526	8.5e-33
TAIR|locus:2094558	881	CFM3A "CRM family member 3A" [	0.726	0.232	0.301	8.8e-21
TAIR|locus:2094997	848	EMB1865 "embryo defective 1865	0.680	0.226	0.334	4.3e-19
TAIR|locus:2096662	1011	CFM2 "CRM family member 2" [Ar	0.953	0.266	0.248	8.4e-18
TAIR|locus:2181372	720	CRS1 "ortholog of maize chloro	0.436	0.170	0.358	3.7e-13

TAIR|locus:2094438 LOH1 "LAG One Homologue 1" [Arabidopsis thaliana (taxid:3702)]

 Score = 830 (297.2 bits), Expect = 8.2e-83, P = 8.2e-83
 Identities = 179/289 (61%), Positives = 210/289 (72%)

Query:     2 THDPEILTPEEHFYFLKMGRKCKNYVPVGRRGIYQGVILNMHLHWKKHQTLKVIVKTFSA 61
             THDPEILTPEEHFY+LKMG KCKNYVPVGRRGIYQGVILNMHLHWKKHQTL+V++KTF+ 
Sbjct:   171 THDPEILTPEEHFYYLKMGLKCKNYVPVGRRGIYQGVILNMHLHWKKHQTLQVVIKTFTP 230

Query:    62 EEVKEIAAELARLTGGIVLEIHEENTIIMYRGKNYAQPPTEIMSPRITLSRKKALDKSKY 121
             +EVKEIA ELARLTGGIVL++HE NTIIMYRGKNY QPPTEIMSPRITL RKKALDKSK 
Sbjct:   231 DEVKEIAVELARLTGGIVLDVHEGNTIIMYRGKNYVQPPTEIMSPRITLPRKKALDKSKC 290

Query:   122 RDGLRAVKKYIPKXXXXXXXXXXXXXTRSENRSDAAEDVQ--NTELDKPDFGSIPSMMEC 179
             RD LRAV+KYIP+             T+ +  +   +D Q  + EL K     I    EC
Sbjct:   291 RDALRAVRKYIPRLEQELQLLQAQAETKRDYTNVKVDDNQERSEELKK----IIERSEEC 346

Query:   180 SENDPTTESL---MASDSEDLSDIFETDSETETEEKAELRPLYLDQFDKFPVQNDEEHED 236
              E++   +     +A+DS DLSDIFETDSE E + K E RPL+L++F+KFP  N+ E ED
Sbjct:   347 LEDEQEEDEAGLELATDS-DLSDIFETDSELE-DAKTE-RPLFLEEFEKFPAINNREDED 403

Query:   237 FEEHLRQISIDSRNAKSLGKDED---SSHFDEVDKMFLRAASLLKKQKR 282
             F         D   AKS G++ D   S +FDEVDKMFLRAA LLKK++R
Sbjct:   404 FG--------DLGKAKSEGEENDDDKSPNFDEVDKMFLRAAFLLKKKRR 444

GO:0003723 "RNA binding" evidence=IEA

GO:0009507 "chloroplast" evidence=ISM

GO:0042761 "very long-chain fatty acid biosynthetic process" evidence=IGI

GO:0050291 "sphingosine N-acyltransferase activity" evidence=IGI

TAIR|locus:2056558 AT2G28480 [Arabidopsis thaliana (taxid:3702)]

 Score = 376 (137.4 bits), Expect = 1.1e-34, P = 1.1e-34
 Identities = 80/212 (37%), Positives = 121/212 (57%)

Query:     5 PEILTPEEHFYFLKMGRKCKNYVPVGRRGIYQGVILNMHLHWKKHQTLKVIVKTFSAEEV 64
             P  +T EE FY  KMG+K  NYVP+GRRG++ GVILNMHLHWKKH+T+KVI       +V
Sbjct:   161 PHEITGEERFYLKKMGQKRSNYVPIGRRGVFGGVILNMHLHWKKHETVKVICNNSKPGQV 220

Query:    65 KEIAAELARLTGGIVLEIHEENTIIMYRGKNYAQPPTEIMSPRITLSRKKALDKSKYRDG 124
             ++ A ELA+L+GG+ + I  ++TII YRGK Y QP  ++MSP  TLS+K+A +KSKY   
Sbjct:   221 QQYAEELAKLSGGVPVNIIGDDTIIFYRGKGYVQP--QVMSPIDTLSKKRAYEKSKYEQS 278

Query:   125 LRAVKKYIPKXXXXXXXXXXXXXTRSE-NRSDAAEDVQNTELDKPDFGSIPSMMECSEND 183
             L +V+ +I                  + N  +    + ++  +          + CS+ D
Sbjct:   279 LESVRHFIAIAEKELELYYRHVALYDDPNNRNPLSILDDSPSESRQHHENEFFLSCSDTD 338

Query:   184 PTTESLMASDSEDLSDIFETDSETETEEKAEL 215
              ++E     + E+L ++ +  S + +  K EL
Sbjct:   339 SSSED--EDEDEELCEL-DNGSSSSSSAKEEL 367

GO:0003723 "RNA binding" evidence=IEA

GO:0008150 "biological_process" evidence=ND

GO:0009507 "chloroplast" evidence=ISM

TAIR|locus:2091458 AT3G27550 [Arabidopsis thaliana (taxid:3702)]

 Score = 337 (123.7 bits), Expect = 4.5e-34, Sum P(2) = 4.5e-34
 Identities = 65/132 (49%), Positives = 92/132 (69%)

Query:     3 HDPEILTPEEHFYFLKMGRKCKNYVPVGRRGIYQGVILNMHLHWKKHQTLKVIVKTFSAE 62
             HDPE+ T E+   F K+G K KNYVPVG RG++ GV+ NMH+HWK H+T++V    F  E
Sbjct:    87 HDPELFTSEQVQAFKKIGFKNKNYVPVGVRGVFGGVVQNMHMHWKFHETVQVCCDNFPKE 146

Query:    63 EVKEIAAELARLTGGIVLEIHEENTIIMYRGKNYAQPPTEIMSPRITLSRKKALDKSKYR 122
             ++KE+A+ +ARL+GG+V+ IH   TIIM+RG+NY QP   I  P  TL+++KAL K+++ 
Sbjct:   147 KIKEMASMIARLSGGVVINIHNVKTIIMFRGRNYRQPKNLI--PVNTLTKRKALFKARFE 204

Query:   123 DGLRAVKKYIPK 134
               L + K  I K
Sbjct:   205 QALESQKLNIKK 216

GO:0003723 "RNA binding" evidence=IEA

GO:0009507 "chloroplast" evidence=ISM

TAIR|locus:2123276 AT4G13070 [Arabidopsis thaliana (taxid:3702)]

 Score = 358 (131.1 bits), Expect = 8.5e-33, P = 8.5e-33
 Identities = 70/133 (52%), Positives = 94/133 (70%)

Query:     3 HDPEILTPEEHFYFLKMGRKCKNYVPVGRRGIYQGVILNMHLHWKKHQTLKVIVKTFSAE 62
             +DPE LT EE  Y  + G K KN+V VGRRG++ GV+LN+HLHWKKH+T+KVI K  +  
Sbjct:   177 YDPESLTEEEQHYLKRTGEKRKNFVLVGRRGVFGGVVLNLHLHWKKHETVKVICKPCNKP 236

Query:    63 -EVKEIAAELARLTGGIVLEIHEENTIIMYRGKNYAQPPTEIMSPRITLSRKKALDKSKY 121
              +V E A ELARL+ GIV+++   NTI++YRGKNY +P  E+MSP  TLS+ KAL+K +Y
Sbjct:   237 GQVHEYAEELARLSKGIVIDVKPNNTIVLYRGKNYVRP--EVMSPVDTLSKDKALEKYRY 294

Query:   122 RDGLRAVKKYIPK 134
                L    ++I K
Sbjct:   295 EQSLEHTSEFIEK 307

GO:0003723 "RNA binding" evidence=IEA

GO:0008150 "biological_process" evidence=ND

GO:0009507 "chloroplast" evidence=ISM

TAIR|locus:2094558 CFM3A "CRM family member 3A" [Arabidopsis thaliana (taxid:3702)]

 Score = 256 (95.2 bits), Expect = 8.8e-21, P = 8.8e-21
 Identities = 64/212 (30%), Positives = 110/212 (51%)

Query:     4 DPEILTPEEHFYFLKMGRKCKNYVPVGRRGIYQGVILNMHLHWKKHQTLKVIVKTFSAEE 63
             DPE +T EE F F K+G K K ++ +GRRG++ G + NMHLHWK  + +K+IVK  + + 
Sbjct:   634 DPESITDEERFMFRKLGLKMKAFLLLGRRGVFDGTVENMHLHWKYRELVKIIVKAKTFDG 693

Query:    64 VKEIAAELARLTGGIVLEIHEEN---TIIMYRGKNYAQPPTEIMSPRITLSRKKALDKSK 120
             VK++A  L   +GGI++ I +      II+YRG++Y +P   ++ P+  L+++KAL +S 
Sbjct:   694 VKKVALALEAESGGILVSIDKVTKGYAIIVYRGQDYKRPT--MLRPKNLLTKRKALARSI 751

Query:   121 YRDGLRAVKKYIPKXXXXXXXXXXXXXTRSENRSDAAEDVQNTELDKPDFGSIPSMMECS 180
                    + K+I                + E  +D  ++    +LD     S     E  
Sbjct:   752 ELQRREGLLKHI-STMQAKAKQLRAEIEQMEKVTDKGDEELYNKLDMAYASSDEETDEED 810

Query:   181 ENDPTTESLMASDSEDLSDIFETD-SETETEE 211
             ++D   E+    +  +  +I   + SETE ++
Sbjct:   811 DDDAFPETYAEGEDGEEGEILAGELSETEDKD 842

GO:0003723 "RNA binding" evidence=IEA

GO:0009507 "chloroplast" evidence=ISM;IDA

GO:0000373 "Group II intron splicing" evidence=IMP

GO:0048316 "seed development" evidence=IGI

TAIR|locus:2094997 EMB1865 "embryo defective 1865" [Arabidopsis thaliana (taxid:3702)]

 Score = 240 (89.5 bits), Expect = 4.3e-19, P = 4.3e-19
 Identities = 68/203 (33%), Positives = 108/203 (53%)

Query:     3 HDPEILTPEEHFYFLKMGRKCKNYVPVGRRGIYQGVILNMHLHWKKHQTLKVIVKTFSAE 62
             +D E+++ EE   F K+G K K Y+P+G RG++ GVI NMHLHWK  + +K+I K  +  
Sbjct:   648 YDQEVISEEERAMFRKVGLKMKAYLPIGIRGVFDGVIENMHLHWKHRELVKLISKQKNQA 707

Query:    63 EVKEIAAELARLTGGIVLEIHEEN---TIIMYRGKNYAQPPTEIMSPRITLSRKKALDKS 119
              V+E A  L   +GG+++ I +      +I YRGKNY +P +  + PR  L++ KAL +S
Sbjct:   708 FVEETARLLEYESGGVLVAIEKVPKGFALIYYRGKNYRRPIS--LRPRNLLTKAKALKRS 765

Query:   120 KYRDGLRAVKKYIPKXXXXXXXXXXXXXTRSENRSDAAEDVQNTELDKPDFGSIPSMMEC 179
                    A+ ++I +               S+N S +  + +N E D  D       +E 
Sbjct:   766 IAMQRHEALSQHISELERTIEQMQSQLT--SKNPSYSESEWENDEDDDDDEEEEKDDVED 823

Query:   180 SEND--PTT-ESLMASDSE-DLS 198
             +E+D   T  ES ++S  E D+S
Sbjct:   824 NESDWDETDGESAISSIEEADMS 846

GO:0003723 "RNA binding" evidence=IEA

GO:0009507 "chloroplast" evidence=ISM;IDA

GO:0009793 "embryo development ending in seed dormancy" evidence=NAS

GO:0009737 "response to abscisic acid stimulus" evidence=IDA

GO:0006655 "phosphatidylglycerol biosynthetic process" evidence=RCA

GO:0009902 "chloroplast relocation" evidence=RCA

GO:0010027 "thylakoid membrane organization" evidence=RCA

GO:0016117 "carotenoid biosynthetic process" evidence=RCA

GO:0019288 "isopentenyl diphosphate biosynthetic process, mevalonate-independent pathway" evidence=RCA

GO:0034660 "ncRNA metabolic process" evidence=RCA

TAIR|locus:2096662 CFM2 "CRM family member 2" [Arabidopsis thaliana (taxid:3702)]

 Score = 229 (85.7 bits), Expect = 8.4e-18, P = 8.4e-18
 Identities = 70/282 (24%), Positives = 129/282 (45%)

Query:     4 DPEILTPEEHFYFLKMGRKCKNYVPVGRRGIYQGVILNMHLHWKKHQTLKVIVKTFSAEE 63
             D E +T +E +   K+G K K ++ +GRRG++ G I NMHLHWK  + +K+I   +S E 
Sbjct:   575 DKEGITNDEKYMLRKIGLKMKPFLLLGRRGVFDGTIENMHLHWKYRELVKIICNEYSIEA 634

Query:    64 VKEIAAELARLTGGIVLEIHEEN---TIIMYRGKNYAQPPTEIMSPRITLSRKKALDKSK 120
               ++A  L   +GGI++ +   +    II+YRGKNY +P  + + P+  LS+++AL +S 
Sbjct:   635 AHKVAEILEAESGGILVAVEMVSKGYAIIVYRGKNYERP--QCLRPQTLLSKREALKRSV 692

Query:   121 YRDGLRAVKKYIPKXXXXXXXXXXXXXTRSENRSDAAEDVQNTELDKPDFGSIPSMMECS 180
                  +++K ++ K               S   ++   D +++ +   +     +  + +
Sbjct:   693 EAQRRKSLKLHVLKLSNNIEELNRQLVEDSAT-NETWSDGESSNMMVEE----ETENQHT 747

Query:   181 ENDPTTESLMASDSEDLSDIFETDSETETEEKAELRPLYLDQFDKFPVQNDEEHEDFEEH 240
             E +   E +    S DLS     +   E + + E+ PL     +    Q DE      + 
Sbjct:   748 EPEKAREKIELGYSSDLSVPSSGEENWEDDSEGEVDPLTTSSQE---YQEDESESASSQR 804

Query:   241 LRQISIDSRNAKSLGKDEDSSHFDEVDKMFLRAASLLKKQKR 282
                 S+DS    S+  +  S++        L   S L   ++
Sbjct:   805 HEGNSLDSTANLSVFAETGSANASSFHDRSLPHNSFLNANRK 846

GO:0003723 "RNA binding" evidence=IEA

GO:0009507 "chloroplast" evidence=ISM;RCA

GO:0000372 "Group I intron splicing" evidence=IMP

GO:0000373 "Group II intron splicing" evidence=IMP

TAIR|locus:2181372 CRS1 "ortholog of maize chloroplast splicing factor CRS1" [Arabidopsis thaliana (taxid:3702)]

 Score = 192 (72.6 bits), Expect = 3.7e-13, P = 3.7e-13
 Identities = 47/131 (35%), Positives = 76/131 (58%)

Query:     4 DPEILTPEEHFYFLKMGRKCKNYVPVGRRGIYQGVILNMHLHWKKHQTLKVIV--KTFSA 61
             D EILT EE     ++G K  + + +GRRG++ GV+  +H HWK  +  KVI   K FS 
Sbjct:   568 DIEILTNEERECLRRIGLKMNSSLVLGRRGVFFGVMEGLHQHWKHREVAKVITMQKLFS- 626

Query:    62 EEVKEIAAELARLTGGIVLEIH---EENTIIMYRGKNYAQPPTEIMSPRITLSRKKALDK 118
               V   A  L   + G+++ I    E + I++YRGKNY +P +++M+  + L+++KAL +
Sbjct:   627 -RVVYTAKALETESNGVLISIEKLKEGHAILIYRGKNYKRPSSKLMAQNL-LTKRKALQR 684

Query:   119 SKYRDGLRAVK 129
             S     L ++K
Sbjct:   685 SVVMQRLGSLK 695


Parameters:
  V=100
  filter=SEG
  E=0.001

  ctxfactor=1.00

  Query                        -----  As Used  -----    -----  Computed  ----
  Frame  MatID Matrix name     Lambda    K       H      Lambda    K       H
   +0      0   BLOSUM62        0.313   0.131   0.367    same    same    same
               Q=9,R=2         0.244   0.0300  0.180     n/a     n/a     n/a

  Query
  Frame  MatID  Length  Eff.Length     E     S W   T  X   E2     S2
   +0      0      282       269   0.00096  114 3  11 23  0.40    34
                                                     32  0.39    37


Statistics:

  Database:  /share/blast/go-seqdb.fasta
   Title:  go_20130330-seqdb.fasta
   Posted:  5:47:42 AM PDT Apr 1, 2013
   Created:  5:47:42 AM PDT Apr 1, 2013
   Format:  XDF-1
   # of letters in database:  169,044,731
   # of sequences in database:  368,745
   # of database sequences satisfying E:  8
  No. of states in DFA:  591 (63 KB)
  Total size of DFA:  192 KB (2110 KB)
  Time to generate neighborhood:  0.00u 0.00s 0.00t   Elapsed:  00:00:00
  No. of threads or processors used:  24
  Search cpu time:  28.19u 0.11s 28.30t   Elapsed:  00:00:02
  Total cpu time:  28.19u 0.11s 28.30t   Elapsed:  00:00:02
  Start:  Fri May 10 03:42:55 2013   End:  Fri May 10 03:42:57 2013

GO:0003723 "RNA binding" evidence=IEA

GO:0009507 "chloroplast" evidence=ISM

GO:0000373 "Group II intron splicing" evidence=IDA

---

Prediction of Enzyme Commission (EC) Number

EC Number Prediction by Annotation Transfer from SWISS-PROT Entries

Original result of BLAST against SWISS-PROT

ID	Name	Annotated EC number	Identity	Query coverage	Hit coverage	RBH(Q2H)	RBH(H2Q)
Q67XL4	Y3544_ARATH	No assigned EC number	0.6643	0.9539	0.6058	yes	no

EC Number Prediction by Ezypred Server

Original result from Ezypred Server

Fail to connect to Ezypred Server

EC Number Prediction by EFICAz Software

No EC number assignment, probably not an enzyme!

---

Prediction of Functionally Associated Proteins

Functionally Associated Proteins Detected by STRING

Original result from the STRING server

Your Input: GSVIVG00035403001 SubName- Full=Chromosome chr12 scaffold_78, whole genome shotgun sequence; (331 aa) (Vitis vinifera)

Predicted Functional Partners:

Sorry, there are no predicted associations at the current settings.

---

Conserved Domains and Related Protein Families

Conserved Domains Detected by RPS-BLAST

Original result of RPS-BLAST against CDD database part I

ID	Length	Definition	E-value
Query	282
smart01103	84	smart01103, CRS1_YhbY, Escherichia coli YhbY is as	1e-22
pfam01985	84	pfam01985, CRS1_YhbY, CRS1 / YhbY (CRM) domain	5e-21

>gnl|CDD|198171 smart01103, CRS1_YhbY, Escherichia coli YhbY is associated with pre-50S ribosomal subunits, which implies a function in ribosome assembly

 Score = 88.7 bits (221), Expect = 1e-22
 Identities = 28/85 (32%), Positives = 46/85 (54%), Gaps = 1/85 (1%)

Query: 8  LTPEEHFYFLKMGRKCKNYVPVGRRGIYQGVILNMHLHWKKHQTLKVIVKTFSAEEVKEI 67
          LT ++  Y   +    K  V +G+ G+ +GV+  +    +KH+ +KV V     E+ KEI
Sbjct: 1  LTGKQKRYLRSLAHHLKPVVQIGKNGLTEGVLEEIDEALEKHELIKVKVLGNDREDRKEI 60

Query: 68 AAELARLTGGIVLEIHEENTIIMYR 92
          A ELA  TG  +++     TI++YR
Sbjct: 61 AEELAEETGAELVQ-VIGKTIVLYR 84

GFP fused to a single-domain CRM protein from maize localises to the nucleolus, suggesting that an analogous activity may have been retained in plants. A CRM domain containing protein in plant chloroplasts has been shown to function in group I and II intron splicing. In vitro experiments with an isolated maize CRM domain have shown it to have RNA binding activity. These and other results suggest that the CRM domain evolved in the context of ribosome function prior to the divergence of Archaea and Bacteria, that this function has been maintained in extant prokaryotes, and that the domain was recruited to serve as an RNA binding module during the evolution of plant genomes. YhbY has a fold similar to that of the C-terminal domain of translation initiation factor 3 (IF3C), which binds to 16S rRNA in the 30S ribosome. Length = 84

>gnl|CDD|190184 pfam01985, CRS1_YhbY, CRS1 / YhbY (CRM) domain

 Score = 84.5 bits (210), Expect = 5e-21
 Identities = 28/85 (32%), Positives = 46/85 (54%), Gaps = 1/85 (1%)

Query: 8  LTPEEHFYFLKMGRKCKNYVPVGRRGIYQGVILNMHLHWKKHQTLKVIVKTFSAEEVKEI 67
          LT ++  Y   +    K  V +G+ G+ +GV+  +    +KH+ +KV V     E+ KEI
Sbjct: 1  LTGKQRRYLRSLAHHLKPVVQIGKNGLTEGVVEEIDEALEKHELIKVKVLGNDREDRKEI 60

Query: 68 AAELARLTGGIVLEIHEENTIIMYR 92
          A ELA  TG  +++     TI++YR
Sbjct: 61 AEELAEKTGAELVQ-VIGRTIVLYR 84

Escherichia coli YhbY is associated with pre-50S ribosomal subunits, which implies a function in ribosome assembly. GFP fused to a single-domain CRM protein from maize localises to the nucleolus, suggesting that an analogous activity may have been retained in plants. A CRM domain containing protein in plant chloroplasts has been shown to function in group I and II intron splicing. In vitro experiments with an isolated maize CRM domain have shown it to have RNA binding activity. These and other results suggest that the CRM domain evolved in the context of ribosome function prior to the divergence of Archaea and Bacteria, that this function has been maintained in extant prokaryotes, and that the domain was recruited to serve as an RNA binding module during the evolution of plant genomes. YhbY has a fold similar to that of the C-terminal domain of translation initiation factor 3 (IF3C), which binds to 16S rRNA in the 30S ribosome. Length = 84

Conserved Domains Detected by HHsearch

Original result of HHsearch against CDD database

ID	Length	Definition	Probability
Query	282
PRK10343	97	RNA-binding protein YhbY; Provisional	99.96
TIGR00253	95	RNA_bind_YhbY putative RNA-binding protein, YhbY f	99.96
PF01985	84	CRS1_YhbY: CRS1 / YhbY (CRM) domain; InterPro: IPR	99.96
COG1534	97	Predicted RNA-binding protein containing KH domain	99.95
KOG1990	564	consensus Poly(A)-specific exoribonuclease PARN [R	99.89
KOG1990	564	consensus Poly(A)-specific exoribonuclease PARN [R	97.73

>PRK10343 RNA-binding protein YhbY; Provisional

Probab=99.96  E-value=1.3e-29  Score=204.07  Aligned_cols=89  Identities=21%  Similarity=0.321  Sum_probs=86.6

Q ss_pred             CCCCHHHHHHHHhcccCCCCeeeecCCCCCHHHHHHHHHHHHhCCeeeEEecCCCHHHHHHHHHHHHHHhCCeEEEEeeC
Q 023463            6 EILTPEEHFYFLKMGRKCKNYVPVGRRGIYQGVILNMHLHWKKHQTLKVIVKTFSAEEVKEIAAELARLTGGIVLEIHEE   85 (282)
Q Consensus         6 E~LT~kQRk~LRklAhkLKPvV~IGK~GVTdgVIeeI~~aLk~HELVKVKv~~~~~ed~keiAeeLe~~TGgeLVqV~IG   85 (282)
                      ++||++||++||++||+|+|+|+||++|||++|+.+|+.+|++||||||++.+++++++++++++||+.|||++|| +||
T Consensus         1 m~Lt~kqr~~LR~~ah~l~Pvv~IGk~Glt~~vi~ei~~aL~~hELIKvkv~~~~~~~~~e~~~~i~~~~~ae~Vq-~IG   79 (97)
T PRK10343          1 MNLSTKQKQHLKGLAHPLKPVVLLGSNGLTEGVLAEIEQALEHHELIKVKIATEDRETKTLIVEAIVRETGACNVQ-VIG   79 (97)
T ss_pred             CCCCHHHHHHHHHhcCCCCCeEEECCCCCCHHHHHHHHHHHHHCCcEEEEecCCChhHHHHHHHHHHHHHCCEEEe-eeC
Confidence            4699999999999999999999999999999999999999999999999999999999999999999999999999 699


Q ss_pred             cEEEEEeCCC
Q 023463           86 NTIIMYRGKN   95 (282)
Q Consensus        86 ~tIILYRgkn   95 (282)
                      +++||||++.
T Consensus        80 ~~~vlYR~~~   89 (97)
T PRK10343         80 KTLVLYRPTK   89 (97)
T ss_pred             cEEEEEecCC
Confidence            9999999975

>TIGR00253 RNA_bind_YhbY putative RNA-binding protein, YhbY family

Probab=99.96  E-value=1.8e-29  Score=202.23  Aligned_cols=87  Identities=28%  Similarity=0.349  Sum_probs=85.1

Q ss_pred             CCHHHHHHHHhcccCCCCeeeecCCCCCHHHHHHHHHHHHhCCeeeEEecCCCHHHHHHHHHHHHHHhCCeEEEEeeCcE
Q 023463            8 LTPEEHFYFLKMGRKCKNYVPVGRRGIYQGVILNMHLHWKKHQTLKVIVKTFSAEEVKEIAAELARLTGGIVLEIHEENT   87 (282)
Q Consensus         8 LT~kQRk~LRklAhkLKPvV~IGK~GVTdgVIeeI~~aLk~HELVKVKv~~~~~ed~keiAeeLe~~TGgeLVqV~IG~t   87 (282)
                      ||++||++||++||+|+|+|+|||+|||++|+++|+.+|++||||||++.++++++++++|.+|++.|||++|| .||++
T Consensus         1 Lt~kqr~~Lr~~ah~l~p~v~IGK~Glt~~vi~ei~~aL~~hELIKVkvl~~~~~~~~e~a~~i~~~~~a~~Vq-~iG~~   79 (95)
T TIGR00253         1 LTGKQKRHLRGKAHHLKPVVLVGKNGLTEGVIKEIEQALEHRELIKVKVATEDREDKTLIAEALVKETGACNVQ-VIGKT   79 (95)
T ss_pred             CCHHHHHHHHHHhCCCCCeEEECCCCCCHHHHHHHHHHHHhCCcEEEEecCCChhHHHHHHHHHHHHHCCEEEE-EEccE
Confidence            79999999999999999999999999999999999999999999999999999999999999999999999999 69999


Q ss_pred             EEEEeCCC
Q 023463           88 IIMYRGKN   95 (282)
Q Consensus        88 IILYRgkn   95 (282)
                      +||||+++
T Consensus        80 ~vlYR~~~   87 (95)
T TIGR00253        80 IVLYRPTK   87 (95)
T ss_pred             EEEEecCC
Confidence            99999974

A combination of crystal structure, molecular modeling, and bioinformatic data together suggest that members of this family, including YhbY of E. coli, are RNA binding proteins.

>PF01985 CRS1_YhbY: CRS1 / YhbY (CRM) domain; InterPro: IPR001890 The CRM domain is an ~100-amino acid RNA-binding domain

Probab=99.96  E-value=7.9e-29  Score=192.36  Aligned_cols=84  Identities=36%  Similarity=0.502  Sum_probs=75.3

Q ss_pred             CCHHHHHHHHhcccCCCCeeeecCCCCCHHHHHHHHHHHHhCCeeeEEecCCCHHHHHHHHHHHHHHhCCeEEEEeeCcE
Q 023463            8 LTPEEHFYFLKMGRKCKNYVPVGRRGIYQGVILNMHLHWKKHQTLKVIVKTFSAEEVKEIAAELARLTGGIVLEIHEENT   87 (282)
Q Consensus         8 LT~kQRk~LRklAhkLKPvV~IGK~GVTdgVIeeI~~aLk~HELVKVKv~~~~~ed~keiAeeLe~~TGgeLVqV~IG~t   87 (282)
                      ||++||++||++||+|+|+|+|||+|||++|+++|+.+|++||||||+|.++++.+++++|+.|++.|||++|+ ++|++
T Consensus         1 Lt~ke~~~Lr~~a~~l~p~v~IGk~Glt~~vi~~i~~~l~~~eLvKVk~~~~~~~~~~~~~~~l~~~t~~~~V~-~iG~~   79 (84)
T PF01985_consen    1 LTSKERKFLRKLAHHLKPVVQIGKNGLTDGVIEEIDDALEKHELVKVKVLGNCREDRKEIAEQLAEKTGAEVVQ-VIGRT   79 (84)
T ss_dssp             --HHHHHHHHHHHTTC--SEEE-TTSS-HHHHHHHHHHHHHHSEEEEEETT--HHHHHHHHHHHHHHHTEEEEE-EETTE
T ss_pred             CCHHHHHHHHHHhcCCCCeEEECCCCCCHHHHHHHHHHHHhCCeeEEEEccCCHHHHHHHHHHHHHHhCCEEEE-EECCE
Confidence            79999999999999999999999999999999999999999999999999999999999999999999999999 79999


Q ss_pred             EEEEe
Q 023463           88 IIMYR   92 (282)
Q Consensus        88 IILYR   92 (282)
                      +||||
T Consensus        80 ~vlyR   84 (84)
T PF01985_consen   80 IVLYR   84 (84)
T ss_dssp             EEEEE
T ss_pred             EEEEC
Confidence            99998

The name chloroplast RNA splicing and ribosome maturation (CRM) has been suggested to reflect the functions established for the four characterised members of the family: Zea mays (Maize) CRS1 (Q9FYT6 from SWISSPROT), CAF1 (Q84N49 from SWISSPROT) and CAF2 (Q84N48 from SWISSPROT) proteins and the Escherichia coli protein YhbY (P0AGK4 from SWISSPROT). The CRM domain is found in eubacteria, archaea, and plants. The CRM domain is represented as a stand-alone protein in archaea and bacteria, and in single- and multi-domain proteins in plants. It has been suggested that prokaryotic CRM proteins existed as ribosome-associated proteins prior to the divergence of archaea and bacteria, and that they were co-opted in the plant lineage as RNA binding modules by incorporation into diverse protein contexts. Plant CRM domains are predicted to reside not only in the chloroplast, but also in the mitochondrion and the nucleo/cytoplasmic compartment. The diversity of the CRM domain family in plants suggests a diverse set of RNA targets [, ]. The CRM domain is a compact alpha/beta domain consisting of a four-stranded beta sheet and three alpha helices with an alpha-beta-alpha-beta-alpha-beta-beta topology. The beta sheet face is basic, consistent with a role in RNA binding. Proximal to the basic beta sheet face is another moiety that could contribute to nucleic acid recognition. Connecting strand beta1 and helix alpha2 is a loop with a six amino acid motif, GxxG flanked by large aliphatic residues, within which one 'x' is typically a basic residue []. Escherichia coli YhbY is associated with pre-50S ribosomal subunits, which implies a function in ribosome assembly. GFP fused to a single-domain CRM protein from maize localises to the nucleolus, suggesting that an analogous activity may have been retained in plants []. A CRM domain containing protein in plant chloroplasts has been shown to function in group I and II intron splicing []. In vitro experiments with an isolated maize CRM domain have shown it to have RNA binding activity. These and other results suggest that the CRM domain evolved in the context of ribosome function prior to the divergence of Archaea and Bacteria, that this function has been maintained in extant prokaryotes, and that the domain was recruited to serve as an RNA binding module during the evolution of plant genomes []. YhbY has a fold similar to that of the C-terminal domain of translation initiation factor 3 (IF3C), which binds to 16S rRNA in the 30S ribosome [].; GO: 0003723 RNA binding; PDB: 1RQ8_A 1JO0_B 1LN4_A.

>COG1534 Predicted RNA-binding protein containing KH domain, possibly ribosomal protein [Translation, ribosomal structure and biogenesis]

Probab=99.95  E-value=1.6e-27  Score=192.24  Aligned_cols=87  Identities=28%  Similarity=0.424  Sum_probs=84.7

Q ss_pred             CCCHHHHHHHHhcccCCCCeeeecCCCCCHHHHHHHHHHHHhCCeeeEEecCCCHHHHHHHHHHHHHHhCCeEEEEeeCc
Q 023463            7 ILTPEEHFYFLKMGRKCKNYVPVGRRGIYQGVILNMHLHWKKHQTLKVIVKTFSAEEVKEIAAELARLTGGIVLEIHEEN   86 (282)
Q Consensus         7 ~LT~kQRk~LRklAhkLKPvV~IGK~GVTdgVIeeI~~aLk~HELVKVKv~~~~~ed~keiAeeLe~~TGgeLVqV~IG~   86 (282)
                      +||++|+++||+.||+++|+|+||++|||++||.+|+.+|++||||||++.+++.++++++|+.|++.+||.+|| .||+
T Consensus         1 ~Lt~kq~~~Lrs~Ah~l~piv~IGk~Glte~vi~Ei~~aL~~reLIKVkvl~~~~edr~eia~~l~~~~~a~lVq-viG~   79 (97)
T COG1534           1 MLTGKQKRFLRSKAHHLKPIVQIGKNGLTEGVIKEIDRALEARELIKVKVLQNAREDKKEIAEALAEETGAELVQ-VIGK   79 (97)
T ss_pred             CCcHHHHHHHHHhhccCCceEEecCCccCHHHHHHHHHHHHhCCcEEEEeeccchhhHHHHHHHHHHHhCCEEee-eeee
Confidence            599999999999999999999999999999999999999999999999999999999999999999999999999 5999


Q ss_pred             EEEEEeCC
Q 023463           87 TIIMYRGK   94 (282)
Q Consensus        87 tIILYRgk   94 (282)
                      ++||||.+
T Consensus        80 ~~vlyr~~   87 (97)
T COG1534          80 TLVLYRES   87 (97)
T ss_pred             EEEEEecC
Confidence            99999943

>KOG1990 consensus Poly(A)-specific exoribonuclease PARN [Replication, recombination and repair]

Probab=99.89  E-value=5.3e-24  Score=212.71  Aligned_cols=150  Identities=44%  Similarity=0.675  Sum_probs=141.8

Q ss_pred             CCCCCCCHHHHHHHHhcccCCCCeeeecCCCCCHHHHHHHHHHHHhCCeeeEEecCCCH-HHHHHHHHHHHHHhCCeEEE
Q 023463            3 HDPEILTPEEHFYFLKMGRKCKNYVPVGRRGIYQGVILNMHLHWKKHQTLKVIVKTFSA-EEVKEIAAELARLTGGIVLE   81 (282)
Q Consensus         3 ~D~E~LT~kQRk~LRklAhkLKPvV~IGK~GVTdgVIeeI~~aLk~HELVKVKv~~~~~-ed~keiAeeLe~~TGgeLVq   81 (282)
                      +|++.+|.+++.+++++|.+|++++.+|++|+++||+.++|.||++||++||+|+.... ..++..|..++..+|+++|+
T Consensus       378 ~~~e~~t~ee~~~~~k~g~k~~~~~~~~rrg~f~g~i~n~~l~wk~~e~~k~i~~~~~~~~~~~~~a~~le~esg~~~v~  457 (564)
T KOG1990|consen  378 YDPESITEEERLMLRKVGLKMKRRLLSGRRGVFDGVIENMHLHWKSRELVKVICKEKNLPSQVKQYASALERESGGILVS  457 (564)
T ss_pred             cchhhcChHHHHHHHHHHHhhccccccCCcccccceeecchhhhhhcccceeeeccccccHHHHHHHHHHHHHhCCceee
Confidence            78999999999999999999999999999999999999999999999999999987655 99999999999999999999


Q ss_pred             E---eeCcEEEEEeCCCCCCCCCccCCcccccchHHHHhHHHHHhhHHHHHHHHHHHHHHHHHHHHHHhhccCCcc
Q 023463           82 I---HEENTIIMYRGKNYAQPPTEIMSPRITLSRKKALDKSKYRDGLRAVKKYIPKLEQELELLRAQAETRSENRS  154 (282)
Q Consensus        82 V---~IG~tIILYRgknY~~P~~~i~~P~~lLsKrkAL~rs~~~qr~~sl~~~i~~~e~~i~~l~~~~~~~~~~~~  154 (282)
                      +   ..|+.|+.|||+||++|.+  ++|.++|+||+|+.+++++|+.+|+++||+.++++++++++++..+..++.
T Consensus       458 ~~~~~~~~ai~~yr~k~y~~p~~--l~P~~~l~~~k~~~~~~~~~~~~a~~~~i~~~~~~~e~~~~~~~~~~~~~~  531 (564)
T KOG1990|consen  458 IDKNPKGYAIIAYRGKNYDRPTS--LRPRNLLSRRKALERSLEEQRKEALKSHISDLEQEIEQLQASVEAMPAINK  531 (564)
T ss_pred             eccCCchhhHHHhhhhhccCCcc--cCchhhhcccCCccccHHHHHHHHHhhhcchhhhhHHHhhcchhccccccc
Confidence            6   3567799999999999977  999999999999999999999999999999999999999999988766655

>KOG1990 consensus Poly(A)-specific exoribonuclease PARN [Replication, recombination and repair]

Probab=97.73  E-value=2.6e-05  Score=79.28  Aligned_cols=97  Identities=30%  Similarity=0.483  Sum_probs=86.0

Q ss_pred             CCCCCCCCHHHHHHHHhcccCCCCeeeecCCCCCHHHHHHHHHHHHhCCeeeEEecC-CCHHHHHHHHHHH--HHHhCCe
Q 023463            2 THDPEILTPEEHFYFLKMGRKCKNYVPVGRRGIYQGVILNMHLHWKKHQTLKVIVKT-FSAEEVKEIAAEL--ARLTGGI   78 (282)
Q Consensus         2 ~~D~E~LT~kQRk~LRklAhkLKPvV~IGK~GVTdgVIeeI~~aLk~HELVKVKv~~-~~~ed~keiAeeL--e~~TGge   78 (282)
                      ...+..||..+--++|.+|-...|++.+|.++.-.++...|..+|..|+..|+.+.. ........++..+  -..+|+.
T Consensus       169 ~~~~~~l~~~~~~~~r~~~~~~p~~~~~~~~~~~~~~~~~~~~~~~k~~~~k~~~~rg~~~~~~~~~a~~l~~~~~tg~~  248 (564)
T KOG1990|consen  169 VGSPPLLTSIESTLLRRLGYKLPPHFALGRSRKLQGLAVAMVSFWEKHEFAKILIKRGVLETRKERMADELQELLLTGKV  248 (564)
T ss_pred             CCChhhhhhHHHHHHHHhcccccccceehhccccccchhHHHHHHHHHHHHHHHHHhcchhhhccchHHHHHHHHhcCCe
Confidence            456778999999999999999999999999999999999999999999999987764 3444556777777  8899999


Q ss_pred             EEEEeeCcEEEEEeCCCCCCC
Q 023463           79 VLEIHEENTIIMYRGKNYAQP   99 (282)
Q Consensus        79 LVqV~IG~tIILYRgknY~~P   99 (282)
                      ||. +-|..+|+||++++-.|
T Consensus       249 lv~-hN~~~dv~y~~~~Fl~~  268 (564)
T KOG1990|consen  249 LVL-HNKLLDVMYRYKNFLSP  268 (564)
T ss_pred             EEe-eccceeeeeehhhcccc
Confidence            997 89999999999999764

---

Homologous Structure Templates

Structure Templates Detected by BLAST

Original result of BLAST against Protein Data Bank

No homologous structure with e-value below 0.005

Structure Templates Detected by RPS-BLAST

Original result of RPS-BLAST against PDB70 database

ID	Length	Definition	E-value
Query	282
1jo0_A	98	Hypothetical protein HI1333; structural genomics,	5e-11
1rq8_A	104	Conserved hypothetical protein; structural genomic	2e-10
1vt4_I	1221	APAF-1 related killer DARK; drosophila apoptosome,	6e-10
1vt4_I	1221	APAF-1 related killer DARK; drosophila apoptosome,	9e-06

>1jo0_A Hypothetical protein HI1333; structural genomics, YHBY_HAEI structure 2 function project, S2F, unknown function; 1.37A {Haemophilus influenzae} SCOP: d.68.4.1 PDB: 1ln4_A Length = 98

 Score = 57.3 bits (139), Expect = 5e-11
 Identities = 20/106 (18%), Positives = 41/106 (38%), Gaps = 10/106 (9%)

Query: 8   LTPEEHFYFLKMGRKCKNYVPVGRRGIYQGVILNMHLHWKKHQTLKVIVKTFSAEEVKEI 67
           L+ ++  +   +       V +G  G+ +GV+  +      H+ +KV V     E  + I
Sbjct: 3   LSTKQKQFLKGLAHHLNPVVMLGGNGLTEGVLAEIENALNHHELIKVKVAGADRETKQLI 62

Query: 68  AAELARLTGGIVLEIHEENTIIMYRGKNYAQPPTEIMSPRITLSRK 113
              + R T    ++    + +++YR              +I L RK
Sbjct: 63  INAIVRETKAAQVQTI-GHILVLYRPSE---------EAKIQLPRK 98

>1rq8_A Conserved hypothetical protein; structural genomics, SAV1595, YHBY, UPF0044, unknown function; NMR {Staphylococcus aureus} SCOP: d.68.4.1 Length = 104

 Score = 55.8 bits (135), Expect = 2e-10
 Identities = 20/109 (18%), Positives = 45/109 (41%), Gaps = 9/109 (8%)

Query: 7   ILTPEEHFYFLKMGRKCKNYVPVGRRGIYQGVILNMHLHWKKHQTLKVIVKTFSAEEVKE 66
           +LT ++  Y   +         +G+ GI + +I  +    +  + +KV V   + ++ KE
Sbjct: 1   MLTGKQKRYLRSLAHNIDPIFQIGKGGINENMIKQIDDTLENRELIKVHVLQNNFDDKKE 60

Query: 67  IAAELARLTGGIVLEIHEENTIIMYRGKNYAQPPTEIMSPRITLSRKKA 115
           +A  L+  T   +++    + I++YR     +         I L  +  
Sbjct: 61  LAETLSEATRSELVQ-VIGSMIVIYR-----ESKEN---KEIELPLEHH 100

>1vt4_I APAF-1 related killer DARK; drosophila apoptosome, apoptosis, programmed cell death; HET: DTP; 6.90A {Drosophila melanogaster} PDB: 3iz8_A* Length = 1221

 Score = 58.7 bits (141), Expect = 6e-10
 Identities = 58/307 (18%), Positives = 94/307 (30%), Gaps = 79/307 (25%)

Query: 42  MHLHWKK--HQTLKVIVKTF-------------SAEEVKEIAAELARLTGG----IVLEI 82
               +K          V  F             S EE+  I      ++G       L  
Sbjct: 14  HQYQYKDILSVFEDAFVDNFDCKDVQDMPKSILSKEEIDHIIMSKDAVSGTLRLFWTLLS 73

Query: 83  HEENTIIMYRG----KNYAQPPTEIMSPRITLSRKKALDKSKY---RDGL----RAVKKY 131
            +E  +  +       NY      +MSP  T  R+ ++    Y   RD L    +   KY
Sbjct: 74  KQEEMVQKFVEEVLRINYKF----LMSPIKTEQRQPSMMTRMYIEQRDRLYNDNQVFAKY 129

Query: 132 -IPKLEQELELLRAQAETRSENR------------SDAAEDVQNTEL-DKPDFGSI--PS 175
            + +L+  L+L +A  E R                  A +   + ++  K DF  I   +
Sbjct: 130 NVSRLQPYLKLRQALLELRPAKNVLIDGVLGSGKTWVALDVCLSYKVQCKMDFK-IFWLN 188

Query: 176 MMECSENDPTTESL------MASDSEDLSDIFETDSETETEEKAELRPLYLDQFDKFP-- 227
           +  C+  +   E L      +  +    SD            +AELR L   +   +   
Sbjct: 189 LKNCNSPETVLEMLQKLLYQIDPNWTSRSDHSSNIKLRIHSIQAELRRLLKSK--PYENC 246

Query: 228 ------VQNDEEHEDFEEH---L---RQISI-DSRNAK-----SLGKDEDSSHFDEVDKM 269
                 VQN +    F      L   R   + D  +A      SL     +   DEV  +
Sbjct: 247 LLVLLNVQNAKAWNAFNLSCKILLTTRFKQVTDFLSAATTTHISLDHHSMTLTPDEVKSL 306

Query: 270 FLRAASL 276
            L+    
Sbjct: 307 LLKYLDC 313

>1vt4_I APAF-1 related killer DARK; drosophila apoptosome, apoptosis, programmed cell death; HET: DTP; 6.90A {Drosophila melanogaster} PDB: 3iz8_A* Length = 1221

 Score = 46.0 bits (108), Expect = 9e-06
 Identities = 53/362 (14%), Positives = 97/362 (26%), Gaps = 120/362 (33%)

Query: 4   DPEILTPEEHFYFLKMGRKCKNYVPVGRRGIYQGVILNMHLHWKKHQTLKVIVKTFSAEE 63
           + +       F        CK  + +  R  ++ V   +      H +L     T + +E
Sbjct: 255 NAKAW---NAFNL-----SCK--ILLTTR--FKQVTDFLSAATTTHISLDHHSMTLTPDE 302

Query: 64  VKEIAA--------ELAR--------LTGGIVLEIHEENTIIMYRGKNYAQPPTEIMSPR 107
           VK +          +L R            I   I +          N+     + ++  
Sbjct: 303 VKSLLLKYLDCRPQDLPREVLTTNPRRLSIIAESIRDGLA----TWDNWKHVNCDKLTTI 358

Query: 108 ITLSRKKALDKSKYRDGLRA-------VKKYIPKLEQELELLRAQAETRSE--------N 152
           I  S    L+ ++YR                IP     L L+                  
Sbjct: 359 IESSLN-VLEPAEYRKMFDRLSVFPPSAH--IP--TILLSLIWFDVIKSDVMVVVNKLHK 413

Query: 153 RSDAAEDVQNTELDKPDFGSIPSM---MECS-ENDPTTESLM--------ASDSEDLSDI 200
            S   +  + + +      SIPS+   ++   EN+      +          DS+DL   
Sbjct: 414 YSLVEKQPKESTI------SIPSIYLELKVKLENEYALHRSIVDHYNIPKTFDSDDLIPP 467

Query: 201 FETD----------SETE-TEEKAELRPLYLD---------------------------- 221
           +                E  E     R ++LD                            
Sbjct: 468 YLDQYFYSHIGHHLKNIEHPERMTLFRMVFLDFRFLEQKIRHDSTAWNASGSILNTLQQL 527

Query: 222 -QFDKFPVQNDEEHE----DFEEHLRQISIDSRNAKSLG------KDEDSSHFDEVDKMF 270
             +  +   ND ++E       + L +I  +   +K           ED + F+E  K  
Sbjct: 528 KFYKPYICDNDPKYERLVNAILDFLPKIEENLICSKYTDLLRIALMAEDEAIFEEAHKQV 587

Query: 271 LR 272
            R
Sbjct: 588 QR 589

Structure Templates Detected by HHsearch

Original result of HHsearch against PDB70 database

ID	Length	Definition	Probability
Query	282
1rq8_A	104	Conserved hypothetical protein; structural genomic	99.97
1jo0_A	98	Hypothetical protein HI1333; structural genomics,	99.97

>1rq8_A Conserved hypothetical protein; structural genomics, SAV1595, YHBY, UPF0044, unknown function; NMR {Staphylococcus aureus} SCOP: d.68.4.1

Probab=99.97  E-value=5.1e-31  Score=213.07  Aligned_cols=88  Identities=20%  Similarity=0.346  Sum_probs=86.4

Q ss_pred             CCCHHHHHHHHhcccCCCCeeeecCCCCCHHHHHHHHHHHHhCCeeeEEecCCCHHHHHHHHHHHHHHhCCeEEEEeeCc
Q 023463            7 ILTPEEHFYFLKMGRKCKNYVPVGRRGIYQGVILNMHLHWKKHQTLKVIVKTFSAEEVKEIAAELARLTGGIVLEIHEEN   86 (282)
Q Consensus         7 ~LT~kQRk~LRklAhkLKPvV~IGK~GVTdgVIeeI~~aLk~HELVKVKv~~~~~ed~keiAeeLe~~TGgeLVqV~IG~   86 (282)
                      |||++||++||++||+|+|+|+|||+|||++|+++|+.+|++||||||+|.++++++++++|++||+.|||++|| +||+
T Consensus         1 mLt~kqr~~LR~~ah~Lkpvv~IGK~GlTe~vi~ei~~aL~~hELIKVkvl~~~~~d~~e~a~~la~~t~a~vVq-~IG~   79 (104)
T 1rq8_A            1 MLTGKQKRYLRSLAHNIDPIFQIGKGGINENMIKQIDDTLENRELIKVHVLQNNFDDKKELAETLSEATRSELVQ-VIGS   79 (104)
T ss_dssp             CCCHHHHHHHHHHTTSSCCSCEECSSSCCHHHHHHHHHHHHHSSEEEEEECCCCHHHHHHHHHHHHHHHTEEEEE-EETT
T ss_pred             CCCHHHHHHHHHHhcCCCCeEEECCCCCCHHHHHHHHHHHHHCCcEEEEEeCCCHHHHHHHHHHHHHHhCCEEEE-EECC
Confidence            799999999999999999999999999999999999999999999999999999999999999999999999999 6999


Q ss_pred             EEEEEeCCC
Q 023463           87 TIIMYRGKN   95 (282)
Q Consensus        87 tIILYRgkn   95 (282)
                      ++||||++.
T Consensus        80 ~~VLYR~~~   88 (104)
T 1rq8_A           80 MIVIYRESK   88 (104)
T ss_dssp             EEEEEECCC
T ss_pred             EEEEEeCCC
Confidence            999999986

>1jo0_A Hypothetical protein HI1333; structural genomics, YHBY_HAEI structure 2 function project, S2F, unknown function; 1.37A {Haemophilus influenzae} SCOP: d.68.4.1 PDB: 1ln4_A

Probab=99.97  E-value=1e-30  Score=208.93  Aligned_cols=89  Identities=18%  Similarity=0.305  Sum_probs=86.5

Q ss_pred             CCCHHHHHHHHhcccCCCCeeeecCCCCCHHHHHHHHHHHHhCCeeeEEecCCCHHHHHHHHHHHHHHhCCeEEEEeeCc
Q 023463            7 ILTPEEHFYFLKMGRKCKNYVPVGRRGIYQGVILNMHLHWKKHQTLKVIVKTFSAEEVKEIAAELARLTGGIVLEIHEEN   86 (282)
Q Consensus         7 ~LT~kQRk~LRklAhkLKPvV~IGK~GVTdgVIeeI~~aLk~HELVKVKv~~~~~ed~keiAeeLe~~TGgeLVqV~IG~   86 (282)
                      .||++||++||++||+|+|+|+|||+|||++|+++|+.||++||||||+|.++++++++++|++|++.|||++|| +||+
T Consensus         2 ~Lt~kqr~~Lr~~ah~l~pvv~IGk~GlT~~vi~ei~~aL~~~ELIKVkvl~~~~~~~~e~a~~la~~t~a~~Vq-~IG~   80 (98)
T 1jo0_A            2 TLSTKQKQFLKGLAHHLNPVVMLGGNGLTEGVLAEIENALNHHELIKVKVAGADRETKQLIINAIVRETKAAQVQ-TIGH   80 (98)
T ss_dssp             CCCHHHHHHHHHHHTTBCCSEEECTTCSCHHHHHHHHHHHHHHSEEEEEETTCCHHHHHHHHHHHHHHHCCEEEE-EETT
T ss_pred             CCCHHHHHHHHHHhcCCCCeEEECCCCCCHHHHHHHHHHHHHCCeEEEEEeCCCHHHHHHHHHHHHHHhCCEEEE-EECC
Confidence            699999999999999999999999999999999999999999999999999999999999999999999999999 6999


Q ss_pred             EEEEEeCCCC
Q 023463           87 TIIMYRGKNY   96 (282)
Q Consensus        87 tIILYRgknY   96 (282)
                      ++||||++..
T Consensus        81 ~~vLyR~~~~   90 (98)
T 1jo0_A           81 ILVLYRPSEE   90 (98)
T ss_dssp             EEEEECCCSS
T ss_pred             EEEEEccCCC
Confidence            9999998743

---

Homologous Structure Domains

Structure Domains Detected by RPS-BLAST

Original result of RPS-BLAST against SCOP70(version1.75) database

ID	Length	Definition	E-value
Query	282
d1rq8a_	96	d.68.4.1 (A:) Hypothetical protein SAV1595 {Staphy	7e-20
d1jo0a_	97	d.68.4.1 (A:) YhbY homologue HI1333 {Haemophilus i	2e-19

>d1rq8a_ d.68.4.1 (A:) Hypothetical protein SAV1595 {Staphylococcus aureus, (strain Mu50 / ATCC 700699) [TaxId: 1280]} Length = 96

class: Alpha and beta proteins (a+b)
fold: IF3-like
superfamily: YhbY-like
family: YhbY-like
domain: Hypothetical protein SAV1595
species: Staphylococcus aureus, (strain Mu50 / ATCC 700699) [TaxId: 1280]

 Score = 80.1 bits (198), Expect = 7e-20
 Identities = 18/90 (20%), Positives = 41/90 (45%), Gaps = 1/90 (1%)

Query: 7  ILTPEEHFYFLKMGRKCKNYVPVGRRGIYQGVILNMHLHWKKHQTLKVIVKTFSAEEVKE 66
          +LT ++  Y   +         +G+ GI + +I  +    +  + +KV V   + ++ KE
Sbjct: 1  MLTGKQKRYLRSLAHNIDPIFQIGKGGINENMIKQIDDTLENRELIKVHVLQNNFDDKKE 60

Query: 67 IAAELARLTGGIVLEIHEENTIIMYRGKNY 96
          +A  L+  T   +++    + I++YR    
Sbjct: 61 LAETLSEATRSELVQ-VIGSMIVIYRESKE 89

>d1jo0a_ d.68.4.1 (A:) YhbY homologue HI1333 {Haemophilus influenzae [TaxId: 727]} Length = 97

class: Alpha and beta proteins (a+b)
fold: IF3-like
superfamily: YhbY-like
family: YhbY-like
domain: YhbY homologue HI1333
species: Haemophilus influenzae [TaxId: 727]

 Score = 79.0 bits (195), Expect = 2e-19
 Identities = 19/100 (19%), Positives = 40/100 (40%), Gaps = 5/100 (5%)

Query: 8   LTPEEHFYFLKMGRKCKNYVPVGRRGIYQGVILNMHLHWKKHQTLKVIVKTFSAEEVKEI 67
           L+ ++  +   +       V +G  G+ +GV+  +      H+ +KV V     E  + I
Sbjct: 3   LSTKQKQFLKGLAHHLNPVVMLGGNGLTEGVLAEIENALNHHELIKVKVAGADRETKQLI 62

Query: 68  AAELARLTGGIVLEIHEENTIIMYRGKNYAQPPTEIMSPR 107
              + R T    ++    + +++YR         +I  PR
Sbjct: 63  INAIVRETKAAQVQ-TIGHILVLYRPS----EEAKIQLPR 97

Homologous Domains Detected by HHsearch

Original result of HHsearch against SCOP70(version1.75) database

ID	Length	Definition	Probability
Query	282
d1jo0a_	97	YhbY homologue HI1333 {Haemophilus influenzae [Tax	99.97
d1rq8a_	96	Hypothetical protein SAV1595 {Staphylococcus aureu	99.97

>d1jo0a_ d.68.4.1 (A:) YhbY homologue HI1333 {Haemophilus influenzae [TaxId: 727]}

class: Alpha and beta proteins (a+b)
fold: IF3-like
superfamily: YhbY-like
family: YhbY-like
domain: YhbY homologue HI1333
species: Haemophilus influenzae [TaxId: 727]

Probab=99.97  E-value=5.4e-31  Score=207.16  Aligned_cols=88  Identities=18%  Similarity=0.319  Sum_probs=86.0

Q ss_pred             CCCHHHHHHHHhcccCCCCeeeecCCCCCHHHHHHHHHHHHhCCeeeEEecCCCHHHHHHHHHHHHHHhCCeEEEEeeCc
Q 023463            7 ILTPEEHFYFLKMGRKCKNYVPVGRRGIYQGVILNMHLHWKKHQTLKVIVKTFSAEEVKEIAAELARLTGGIVLEIHEEN   86 (282)
Q Consensus         7 ~LT~kQRk~LRklAhkLKPvV~IGK~GVTdgVIeeI~~aLk~HELVKVKv~~~~~ed~keiAeeLe~~TGgeLVqV~IG~   86 (282)
                      +||++||++||++||+|+|+|+||++|||++|+.+|+.+|++||||||+|.+++++++++++++|++.|||.||| .||+
T Consensus         2 tLt~kqr~~LR~~ah~lkp~v~IGk~Glt~~vi~ei~~al~~~ELIKvki~~~~~~~~~~~~~~l~~~t~~~vV~-~iG~   80 (97)
T d1jo0a_           2 TLSTKQKQFLKGLAHHLNPVVMLGGNGLTEGVLAEIENALNHHELIKVKVAGADRETKQLIINAIVRETKAAQVQ-TIGH   80 (97)
T ss_dssp             CCCHHHHHHHHHHHTTBCCSEEECTTCSCHHHHHHHHHHHHHHSEEEEEETTCCHHHHHHHHHHHHHHHCCEEEE-EETT
T ss_pred             CCCHHHHHHHHHHhcCCCCEEEECCCCCCHHHHHHHHHHHHhCCeEEEEEcCCCHHHHHHHHHHHHHHhCCEEEE-EECC
Confidence            699999999999999999999999999999999999999999999999999999999999999999999999999 6999


Q ss_pred             EEEEEeCCC
Q 023463           87 TIIMYRGKN   95 (282)
Q Consensus        87 tIILYRgkn   95 (282)
                      ++||||+++
T Consensus        81 ~~ilYR~~~   89 (97)
T d1jo0a_          81 ILVLYRPSE   89 (97)
T ss_dssp             EEEEECCCS
T ss_pred             EEEEEcCCC
Confidence            999999865

>d1rq8a_ d.68.4.1 (A:) Hypothetical protein SAV1595 {Staphylococcus aureus, (strain Mu50 / ATCC 700699) [TaxId: 1280]}

class: Alpha and beta proteins (a+b)
fold: IF3-like
superfamily: YhbY-like
family: YhbY-like
domain: Hypothetical protein SAV1595
species: Staphylococcus aureus, (strain Mu50 / ATCC 700699) [TaxId: 1280]

Probab=99.97  E-value=8.6e-31  Score=205.65  Aligned_cols=89  Identities=20%  Similarity=0.332  Sum_probs=86.9

Q ss_pred             CCCHHHHHHHHhcccCCCCeeeecCCCCCHHHHHHHHHHHHhCCeeeEEecCCCHHHHHHHHHHHHHHhCCeEEEEeeCc
Q 023463            7 ILTPEEHFYFLKMGRKCKNYVPVGRRGIYQGVILNMHLHWKKHQTLKVIVKTFSAEEVKEIAAELARLTGGIVLEIHEEN   86 (282)
Q Consensus         7 ~LT~kQRk~LRklAhkLKPvV~IGK~GVTdgVIeeI~~aLk~HELVKVKv~~~~~ed~keiAeeLe~~TGgeLVqV~IG~   86 (282)
                      |||++||++||++||+|+|+|+||++|||++|+.+|+.+|++||||||+|.+++..+++++|++||+.|||++|| +||+
T Consensus         1 mLt~kqr~~LR~~ah~l~p~v~IGk~Glt~~vi~ei~~~l~~~ELIKvk~~~~~~~~~~~~~~~l~~~t~a~~V~-~iG~   79 (96)
T d1rq8a_           1 MLTGKQKRYLRSLAHNIDPIFQIGKGGINENMIKQIDDTLENRELIKVHVLQNNFDDKKELAETLSEATRSELVQ-VIGS   79 (96)
T ss_dssp             CCCHHHHHHHHHHTTSSCCSCEECSSSCCHHHHHHHHHHHHHSSEEEEEECCCCHHHHHHHHHHHHHHHTEEEEE-EETT
T ss_pred             CcCHHHHHHHHHHhcCCCCEEEECCCCCCHHHHHHHHHHHHhCCeeEEEecCCCHHHHHHHHHHHHHHhCCEEEE-EECC
Confidence            799999999999999999999999999999999999999999999999999999999999999999999999999 6999


Q ss_pred             EEEEEeCCCC
Q 023463           87 TIIMYRGKNY   96 (282)
Q Consensus        87 tIILYRgknY   96 (282)
                      ++||||++++
T Consensus        80 ~~vlyR~~~~   89 (96)
T d1rq8a_          80 MIVIYRESKE   89 (96)
T ss_dssp             EEEEEECCCS
T ss_pred             EEEEEeCCCC
Confidence            9999999765